├── .devcontainer └── devcontainer.json ├── .editorconfig ├── .gitattributes ├── .github ├── .dockstore.yml ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE │ ├── bug_report.yml │ └── feature_request.yml ├── PULL_REQUEST_TEMPLATE.md └── workflows │ ├── ci.yml │ ├── fix-linting.yml │ ├── linting.yml │ └── linting_comment.yml ├── .gitignore ├── .gitpod.yml ├── .nf-core.yml ├── .pre-commit-config.yaml ├── .prettierignore ├── .prettierrc.yml ├── CHANGELOG.md ├── CITATIONS.md ├── LICENSE ├── README.md ├── assets ├── adaptivecard.json ├── dincalcilab-samurai_logo_dark.png ├── dincalcilab-samurai_logo_light.png ├── email_template.html ├── email_template.txt ├── ichorcna │ ├── GRCh38.GCA_000001405.2_centromere_acen.txt │ ├── HD_ULP_PoN_hg38_500kb_median_normAutosome_median.rds │ ├── Koren_repTiming_hg38_500kb.wig │ ├── gc_hg38_500kb.wig │ └── map_hg38_500kb.wig ├── methods_description_template.yml ├── multiqc_config.yml ├── samplesheet.csv ├── samurai_logo.png ├── samurai_logo_mqc.png ├── schema_input.json ├── sendmail_template.txt └── slackreport.json ├── bin ├── assemble_aberrations.py ├── assemble_outputs.py ├── assemble_statistics.py ├── check_samplesheet.py ├── compute_signatures.R ├── convert_segment.py ├── correct_logR_ichorcna.R ├── correct_logr_ichorcna.py ├── createPanelOfNormals.R ├── plot_ichorcna_output.R ├── runIchorCNA.R ├── run_ascatsc.R ├── run_hrdcna.R ├── run_maftools.R └── run_qdnaseq.R ├── conf ├── base.config ├── docker_modules.config ├── igenomes.config ├── igenomes_ignored.config ├── modules.config ├── test.config ├── test_full.config └── test_ichorcna.config ├── docs ├── README.md ├── images │ ├── mqc_fastqc_adapter.png │ ├── mqc_fastqc_counts.png │ ├── mqc_fastqc_quality.png │ ├── samurai_logo.png │ └── samurai_map.png ├── output.md └── usage.md ├── main.nf ├── modules.json ├── modules ├── local │ ├── aggregate_ichorcna_table │ │ └── main.nf │ ├── ascat_sc │ │ └── main.nf │ ├── assemble_gistic_output │ │ └── main.nf │ ├── assemble_wisecondorx_outputs │ │ └── main.nf │ ├── cin_signature_quantification │ │ └── main.nf │ ├── concatenate_pdf │ │ └── main.nf │ ├── convert_gistic_seg │ │ └── main.nf │ ├── convert_wisecondorx_images │ │ └── main.nf │ ├── correct_logR_ichorcna │ │ └── main.nf │ ├── create_ascatsc_summary │ │ └── main.nf │ ├── create_qdnaseq_summary │ │ └── main.nf │ ├── deeptools │ │ ├── bampefragmentsize │ │ │ └── main.nf │ │ └── main.nf │ ├── gistic2 │ │ └── main.nf │ ├── hrdcna │ │ └── main.nf │ ├── ichorcna │ │ ├── create_pon │ │ │ └── main.nf │ │ └── run │ │ │ └── main.nf │ ├── maftools │ │ └── main.nf │ ├── plot_ichorcna │ │ └── main.nf │ ├── qdnaseq │ │ └── main.nf │ └── sambamba │ │ └── filterfragment │ │ └── main.nf └── nf-core │ ├── bowtie2 │ ├── align │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── cram_crai.config │ │ │ ├── large_index.config │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── sam.config │ │ │ └── sam2.config │ └── build │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── bwa │ ├── index │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── mem │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── bwamem2 │ ├── index │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── mem │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── dragmap │ ├── align │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── hashtable │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── fastp │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ ├── nextflow.interleaved.config │ │ └── nextflow.save_failed.config │ ├── fastqc │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── hmmcopy │ └── readcounter │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── multiqc │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── picard │ ├── collecthsmetrics │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── collectmultiplemetrics │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── collectwgsmetrics │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── markduplicates │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── samtools │ ├── faidx │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── nextflow2.config │ ├── flagstat │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── idxstats │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── index │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── csi.nextflow.config │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ ├── sort │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ ├── nextflow.config │ │ │ └── nextflow_cram.config │ ├── stats │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ └── view │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── bam.config │ │ ├── bam_index.config │ │ ├── cram_index.config │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── snapaligner │ ├── align │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ │ ├── main.nf.test │ │ │ ├── main.nf.test.snap │ │ │ └── nextflow.config │ └── index │ │ ├── environment.yml │ │ ├── main.nf │ │ ├── meta.yml │ │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── strobealign │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ ├── strobealign.diff │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ └── wisecondorx │ ├── convert │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── newref │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ └── predict │ ├── environment.yml │ ├── main.nf │ ├── meta.yml │ ├── tests │ ├── main.nf.test │ └── main.nf.test.snap │ └── wisecondorx-predict.diff ├── nextflow.config ├── nextflow_schema.json ├── nf-test.config ├── pyproject.toml ├── subworkflows ├── local │ ├── build_pon │ │ ├── main.nf │ │ └── meta.yml │ ├── ichorcna │ │ └── main.nf │ ├── liquid_biopsy │ │ └── main.nf │ ├── run_gistic │ │ └── main.nf │ ├── size_selection │ │ └── main.nf │ ├── solid_biopsy │ │ └── main.nf │ └── utils_samurai_pipeline │ │ └── main.nf └── nf-core │ ├── bam_cnv_wisecondorx │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── bam_markduplicates_picard │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── bam_qc_picard │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── bam_sort_stats_samtools │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── bam_stats_samtools │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── fasta_index_dna │ ├── fasta_index_dna.diff │ ├── main.nf │ └── meta.yml │ ├── fastq_align_bwa │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ ├── main.nf.test.snap │ │ └── nextflow.config │ ├── fastq_align_dna │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── fastq_trim_fastp_fastqc │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.nf.test │ │ └── main.nf.test.snap │ ├── utils_nextflow_pipeline │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.function.nf.test │ │ ├── main.function.nf.test.snap │ │ ├── main.workflow.nf.test │ │ └── nextflow.config │ ├── utils_nfcore_pipeline │ ├── main.nf │ ├── meta.yml │ └── tests │ │ ├── main.function.nf.test │ │ ├── main.function.nf.test.snap │ │ ├── main.workflow.nf.test │ │ ├── main.workflow.nf.test.snap │ │ └── nextflow.config │ └── utils_nfschema_plugin │ ├── main.nf │ ├── meta.yml │ └── tests │ ├── main.nf.test │ ├── nextflow.config │ └── nextflow_schema.json ├── tests └── nextflow.config └── workflows └── samurai.nf /.devcontainer/devcontainer.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/.devcontainer/devcontainer.json -------------------------------------------------------------------------------- /.editorconfig: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/.editorconfig -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/.gitattributes -------------------------------------------------------------------------------- /.github/.dockstore.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/.github/.dockstore.yml -------------------------------------------------------------------------------- /.github/CONTRIBUTING.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/.github/CONTRIBUTING.md -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/bug_report.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/.github/ISSUE_TEMPLATE/bug_report.yml -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/feature_request.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/.github/ISSUE_TEMPLATE/feature_request.yml -------------------------------------------------------------------------------- /.github/PULL_REQUEST_TEMPLATE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/.github/PULL_REQUEST_TEMPLATE.md -------------------------------------------------------------------------------- /.github/workflows/ci.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/.github/workflows/ci.yml -------------------------------------------------------------------------------- /.github/workflows/fix-linting.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/.github/workflows/fix-linting.yml -------------------------------------------------------------------------------- /.github/workflows/linting.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/.github/workflows/linting.yml -------------------------------------------------------------------------------- /.github/workflows/linting_comment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/.github/workflows/linting_comment.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/.gitignore -------------------------------------------------------------------------------- /.gitpod.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/.gitpod.yml -------------------------------------------------------------------------------- /.nf-core.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/.nf-core.yml -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/.pre-commit-config.yaml -------------------------------------------------------------------------------- /.prettierignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/.prettierignore -------------------------------------------------------------------------------- /.prettierrc.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/.prettierrc.yml -------------------------------------------------------------------------------- /CHANGELOG.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/CHANGELOG.md -------------------------------------------------------------------------------- /CITATIONS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/CITATIONS.md -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/README.md -------------------------------------------------------------------------------- /assets/adaptivecard.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/assets/adaptivecard.json -------------------------------------------------------------------------------- /assets/dincalcilab-samurai_logo_dark.png: -------------------------------------------------------------------------------- 1 | samurai_logo_mqc.png -------------------------------------------------------------------------------- /assets/dincalcilab-samurai_logo_light.png: -------------------------------------------------------------------------------- 1 | samurai_logo_mqc.png -------------------------------------------------------------------------------- /assets/email_template.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/assets/email_template.html -------------------------------------------------------------------------------- /assets/email_template.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/assets/email_template.txt -------------------------------------------------------------------------------- /assets/ichorcna/GRCh38.GCA_000001405.2_centromere_acen.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/assets/ichorcna/GRCh38.GCA_000001405.2_centromere_acen.txt -------------------------------------------------------------------------------- /assets/ichorcna/HD_ULP_PoN_hg38_500kb_median_normAutosome_median.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/assets/ichorcna/HD_ULP_PoN_hg38_500kb_median_normAutosome_median.rds -------------------------------------------------------------------------------- /assets/ichorcna/Koren_repTiming_hg38_500kb.wig: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/assets/ichorcna/Koren_repTiming_hg38_500kb.wig -------------------------------------------------------------------------------- /assets/ichorcna/gc_hg38_500kb.wig: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/assets/ichorcna/gc_hg38_500kb.wig -------------------------------------------------------------------------------- /assets/ichorcna/map_hg38_500kb.wig: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/assets/ichorcna/map_hg38_500kb.wig -------------------------------------------------------------------------------- /assets/methods_description_template.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/assets/methods_description_template.yml -------------------------------------------------------------------------------- /assets/multiqc_config.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/assets/multiqc_config.yml -------------------------------------------------------------------------------- /assets/samplesheet.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/assets/samplesheet.csv -------------------------------------------------------------------------------- /assets/samurai_logo.png: -------------------------------------------------------------------------------- 1 | samurai_logo_mqc.png -------------------------------------------------------------------------------- /assets/samurai_logo_mqc.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/assets/samurai_logo_mqc.png -------------------------------------------------------------------------------- /assets/schema_input.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/assets/schema_input.json -------------------------------------------------------------------------------- /assets/sendmail_template.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/assets/sendmail_template.txt -------------------------------------------------------------------------------- /assets/slackreport.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/assets/slackreport.json -------------------------------------------------------------------------------- /bin/assemble_aberrations.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/bin/assemble_aberrations.py -------------------------------------------------------------------------------- /bin/assemble_outputs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/bin/assemble_outputs.py -------------------------------------------------------------------------------- /bin/assemble_statistics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/bin/assemble_statistics.py -------------------------------------------------------------------------------- /bin/check_samplesheet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/bin/check_samplesheet.py -------------------------------------------------------------------------------- /bin/compute_signatures.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/bin/compute_signatures.R -------------------------------------------------------------------------------- /bin/convert_segment.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/bin/convert_segment.py -------------------------------------------------------------------------------- /bin/correct_logR_ichorcna.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/bin/correct_logR_ichorcna.R -------------------------------------------------------------------------------- /bin/correct_logr_ichorcna.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/bin/correct_logr_ichorcna.py -------------------------------------------------------------------------------- /bin/createPanelOfNormals.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/bin/createPanelOfNormals.R -------------------------------------------------------------------------------- /bin/plot_ichorcna_output.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/bin/plot_ichorcna_output.R -------------------------------------------------------------------------------- /bin/runIchorCNA.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/bin/runIchorCNA.R -------------------------------------------------------------------------------- /bin/run_ascatsc.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/bin/run_ascatsc.R -------------------------------------------------------------------------------- /bin/run_hrdcna.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/bin/run_hrdcna.R -------------------------------------------------------------------------------- /bin/run_maftools.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/bin/run_maftools.R -------------------------------------------------------------------------------- /bin/run_qdnaseq.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/bin/run_qdnaseq.R -------------------------------------------------------------------------------- /conf/base.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/conf/base.config -------------------------------------------------------------------------------- /conf/docker_modules.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/conf/docker_modules.config -------------------------------------------------------------------------------- /conf/igenomes.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/conf/igenomes.config -------------------------------------------------------------------------------- /conf/igenomes_ignored.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/conf/igenomes_ignored.config -------------------------------------------------------------------------------- /conf/modules.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/conf/modules.config -------------------------------------------------------------------------------- /conf/test.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/conf/test.config -------------------------------------------------------------------------------- /conf/test_full.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/conf/test_full.config -------------------------------------------------------------------------------- /conf/test_ichorcna.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/conf/test_ichorcna.config -------------------------------------------------------------------------------- /docs/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/docs/README.md -------------------------------------------------------------------------------- /docs/images/mqc_fastqc_adapter.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/docs/images/mqc_fastqc_adapter.png -------------------------------------------------------------------------------- /docs/images/mqc_fastqc_counts.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/docs/images/mqc_fastqc_counts.png -------------------------------------------------------------------------------- /docs/images/mqc_fastqc_quality.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/docs/images/mqc_fastqc_quality.png -------------------------------------------------------------------------------- /docs/images/samurai_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/docs/images/samurai_logo.png -------------------------------------------------------------------------------- /docs/images/samurai_map.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/docs/images/samurai_map.png -------------------------------------------------------------------------------- /docs/output.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/docs/output.md -------------------------------------------------------------------------------- /docs/usage.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/docs/usage.md -------------------------------------------------------------------------------- /main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/main.nf -------------------------------------------------------------------------------- /modules.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules.json -------------------------------------------------------------------------------- /modules/local/aggregate_ichorcna_table/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/local/aggregate_ichorcna_table/main.nf -------------------------------------------------------------------------------- /modules/local/ascat_sc/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/local/ascat_sc/main.nf -------------------------------------------------------------------------------- /modules/local/assemble_gistic_output/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/local/assemble_gistic_output/main.nf -------------------------------------------------------------------------------- /modules/local/assemble_wisecondorx_outputs/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/local/assemble_wisecondorx_outputs/main.nf -------------------------------------------------------------------------------- /modules/local/cin_signature_quantification/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/local/cin_signature_quantification/main.nf -------------------------------------------------------------------------------- /modules/local/concatenate_pdf/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/local/concatenate_pdf/main.nf -------------------------------------------------------------------------------- /modules/local/convert_gistic_seg/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/local/convert_gistic_seg/main.nf -------------------------------------------------------------------------------- /modules/local/convert_wisecondorx_images/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/local/convert_wisecondorx_images/main.nf -------------------------------------------------------------------------------- /modules/local/correct_logR_ichorcna/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/local/correct_logR_ichorcna/main.nf -------------------------------------------------------------------------------- /modules/local/create_ascatsc_summary/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/local/create_ascatsc_summary/main.nf -------------------------------------------------------------------------------- /modules/local/create_qdnaseq_summary/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/local/create_qdnaseq_summary/main.nf -------------------------------------------------------------------------------- /modules/local/deeptools/bampefragmentsize/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/local/deeptools/bampefragmentsize/main.nf -------------------------------------------------------------------------------- /modules/local/deeptools/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/local/deeptools/main.nf -------------------------------------------------------------------------------- /modules/local/gistic2/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/local/gistic2/main.nf -------------------------------------------------------------------------------- /modules/local/hrdcna/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/local/hrdcna/main.nf -------------------------------------------------------------------------------- /modules/local/ichorcna/create_pon/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/local/ichorcna/create_pon/main.nf -------------------------------------------------------------------------------- /modules/local/ichorcna/run/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/local/ichorcna/run/main.nf -------------------------------------------------------------------------------- /modules/local/maftools/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/local/maftools/main.nf -------------------------------------------------------------------------------- /modules/local/plot_ichorcna/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/local/plot_ichorcna/main.nf -------------------------------------------------------------------------------- /modules/local/qdnaseq/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/local/qdnaseq/main.nf -------------------------------------------------------------------------------- /modules/local/sambamba/filterfragment/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/local/sambamba/filterfragment/main.nf -------------------------------------------------------------------------------- /modules/nf-core/bowtie2/align/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bowtie2/align/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/bowtie2/align/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bowtie2/align/main.nf -------------------------------------------------------------------------------- /modules/nf-core/bowtie2/align/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bowtie2/align/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/bowtie2/align/tests/cram_crai.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bowtie2/align/tests/cram_crai.config -------------------------------------------------------------------------------- /modules/nf-core/bowtie2/align/tests/large_index.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bowtie2/align/tests/large_index.config -------------------------------------------------------------------------------- /modules/nf-core/bowtie2/align/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bowtie2/align/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/bowtie2/align/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bowtie2/align/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/bowtie2/align/tests/sam.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bowtie2/align/tests/sam.config -------------------------------------------------------------------------------- /modules/nf-core/bowtie2/align/tests/sam2.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bowtie2/align/tests/sam2.config -------------------------------------------------------------------------------- /modules/nf-core/bowtie2/build/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bowtie2/build/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/bowtie2/build/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bowtie2/build/main.nf -------------------------------------------------------------------------------- /modules/nf-core/bowtie2/build/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bowtie2/build/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/bowtie2/build/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bowtie2/build/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/bowtie2/build/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bowtie2/build/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/bwa/index/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bwa/index/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/bwa/index/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bwa/index/main.nf -------------------------------------------------------------------------------- /modules/nf-core/bwa/index/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bwa/index/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/bwa/index/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bwa/index/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/bwa/index/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bwa/index/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/bwa/mem/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bwa/mem/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/bwa/mem/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bwa/mem/main.nf -------------------------------------------------------------------------------- /modules/nf-core/bwa/mem/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bwa/mem/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/bwa/mem/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bwa/mem/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/bwa/mem/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bwa/mem/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/bwamem2/index/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bwamem2/index/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/bwamem2/index/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bwamem2/index/main.nf -------------------------------------------------------------------------------- /modules/nf-core/bwamem2/index/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bwamem2/index/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/bwamem2/index/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bwamem2/index/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/bwamem2/index/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bwamem2/index/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/bwamem2/mem/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bwamem2/mem/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/bwamem2/mem/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bwamem2/mem/main.nf -------------------------------------------------------------------------------- /modules/nf-core/bwamem2/mem/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bwamem2/mem/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/bwamem2/mem/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bwamem2/mem/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/bwamem2/mem/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/bwamem2/mem/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/dragmap/align/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/dragmap/align/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/dragmap/align/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/dragmap/align/main.nf -------------------------------------------------------------------------------- /modules/nf-core/dragmap/align/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/dragmap/align/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/dragmap/align/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/dragmap/align/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/dragmap/align/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/dragmap/align/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/dragmap/hashtable/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/dragmap/hashtable/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/dragmap/hashtable/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/dragmap/hashtable/main.nf -------------------------------------------------------------------------------- /modules/nf-core/dragmap/hashtable/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/dragmap/hashtable/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/dragmap/hashtable/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/dragmap/hashtable/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/dragmap/hashtable/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/dragmap/hashtable/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/fastp/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/fastp/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/fastp/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/fastp/main.nf -------------------------------------------------------------------------------- /modules/nf-core/fastp/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/fastp/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/fastp/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/fastp/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/fastp/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/fastp/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/fastp/tests/nextflow.interleaved.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/fastp/tests/nextflow.interleaved.config -------------------------------------------------------------------------------- /modules/nf-core/fastp/tests/nextflow.save_failed.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/fastp/tests/nextflow.save_failed.config -------------------------------------------------------------------------------- /modules/nf-core/fastqc/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/fastqc/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/fastqc/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/fastqc/main.nf -------------------------------------------------------------------------------- /modules/nf-core/fastqc/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/fastqc/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/fastqc/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/fastqc/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/fastqc/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/fastqc/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/hmmcopy/readcounter/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/hmmcopy/readcounter/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/hmmcopy/readcounter/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/hmmcopy/readcounter/main.nf -------------------------------------------------------------------------------- /modules/nf-core/hmmcopy/readcounter/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/hmmcopy/readcounter/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/hmmcopy/readcounter/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/hmmcopy/readcounter/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/hmmcopy/readcounter/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/hmmcopy/readcounter/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/multiqc/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/multiqc/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/multiqc/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/multiqc/main.nf -------------------------------------------------------------------------------- /modules/nf-core/multiqc/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/multiqc/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/multiqc/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/multiqc/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/multiqc/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/multiqc/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/multiqc/tests/nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/multiqc/tests/nextflow.config -------------------------------------------------------------------------------- /modules/nf-core/picard/collecthsmetrics/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/picard/collecthsmetrics/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/picard/collecthsmetrics/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/picard/collecthsmetrics/main.nf -------------------------------------------------------------------------------- /modules/nf-core/picard/collecthsmetrics/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/picard/collecthsmetrics/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/picard/collecthsmetrics/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/picard/collectmultiplemetrics/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/picard/collectmultiplemetrics/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/picard/collectmultiplemetrics/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/picard/collectmultiplemetrics/main.nf -------------------------------------------------------------------------------- /modules/nf-core/picard/collectmultiplemetrics/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/picard/collectmultiplemetrics/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/picard/collectwgsmetrics/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/picard/collectwgsmetrics/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/picard/collectwgsmetrics/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/picard/collectwgsmetrics/main.nf -------------------------------------------------------------------------------- /modules/nf-core/picard/collectwgsmetrics/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/picard/collectwgsmetrics/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/picard/markduplicates/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/picard/markduplicates/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/picard/markduplicates/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/picard/markduplicates/main.nf -------------------------------------------------------------------------------- /modules/nf-core/picard/markduplicates/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/picard/markduplicates/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/picard/markduplicates/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/picard/markduplicates/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/picard/markduplicates/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/picard/markduplicates/tests/nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/picard/markduplicates/tests/nextflow.config -------------------------------------------------------------------------------- /modules/nf-core/samtools/faidx/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/faidx/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/samtools/faidx/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/faidx/main.nf -------------------------------------------------------------------------------- /modules/nf-core/samtools/faidx/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/faidx/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/samtools/faidx/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/faidx/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/samtools/faidx/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/faidx/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/samtools/faidx/tests/nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/faidx/tests/nextflow.config -------------------------------------------------------------------------------- /modules/nf-core/samtools/faidx/tests/nextflow2.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/faidx/tests/nextflow2.config -------------------------------------------------------------------------------- /modules/nf-core/samtools/flagstat/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/flagstat/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/samtools/flagstat/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/flagstat/main.nf -------------------------------------------------------------------------------- /modules/nf-core/samtools/flagstat/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/flagstat/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/samtools/flagstat/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/flagstat/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/samtools/flagstat/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/samtools/idxstats/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/idxstats/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/samtools/idxstats/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/idxstats/main.nf -------------------------------------------------------------------------------- /modules/nf-core/samtools/idxstats/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/idxstats/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/samtools/idxstats/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/idxstats/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/samtools/idxstats/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/samtools/index/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/index/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/samtools/index/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/index/main.nf -------------------------------------------------------------------------------- /modules/nf-core/samtools/index/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/index/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/samtools/index/tests/csi.nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/index/tests/csi.nextflow.config -------------------------------------------------------------------------------- /modules/nf-core/samtools/index/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/index/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/samtools/index/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/index/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/samtools/sort/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/sort/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/samtools/sort/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/sort/main.nf -------------------------------------------------------------------------------- /modules/nf-core/samtools/sort/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/sort/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/samtools/sort/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/sort/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/samtools/sort/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/sort/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/samtools/sort/tests/nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/sort/tests/nextflow.config -------------------------------------------------------------------------------- /modules/nf-core/samtools/sort/tests/nextflow_cram.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/sort/tests/nextflow_cram.config -------------------------------------------------------------------------------- /modules/nf-core/samtools/stats/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/stats/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/samtools/stats/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/stats/main.nf -------------------------------------------------------------------------------- /modules/nf-core/samtools/stats/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/stats/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/samtools/stats/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/stats/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/samtools/stats/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/stats/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/samtools/view/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/view/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/samtools/view/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/view/main.nf -------------------------------------------------------------------------------- /modules/nf-core/samtools/view/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/view/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/samtools/view/tests/bam.config: -------------------------------------------------------------------------------- 1 | process { 2 | ext.args = "--output-fmt bam" 3 | } -------------------------------------------------------------------------------- /modules/nf-core/samtools/view/tests/bam_index.config: -------------------------------------------------------------------------------- 1 | process { 2 | ext.args = "--output-fmt bam --write-index" 3 | } -------------------------------------------------------------------------------- /modules/nf-core/samtools/view/tests/cram_index.config: -------------------------------------------------------------------------------- 1 | process { 2 | ext.args = "--output-fmt cram --write-index" 3 | } 4 | -------------------------------------------------------------------------------- /modules/nf-core/samtools/view/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/view/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/samtools/view/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/samtools/view/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/snapaligner/align/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/snapaligner/align/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/snapaligner/align/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/snapaligner/align/main.nf -------------------------------------------------------------------------------- /modules/nf-core/snapaligner/align/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/snapaligner/align/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/snapaligner/align/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/snapaligner/align/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/snapaligner/align/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/snapaligner/align/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/snapaligner/align/tests/nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/snapaligner/align/tests/nextflow.config -------------------------------------------------------------------------------- /modules/nf-core/snapaligner/index/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/snapaligner/index/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/snapaligner/index/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/snapaligner/index/main.nf -------------------------------------------------------------------------------- /modules/nf-core/snapaligner/index/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/snapaligner/index/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/snapaligner/index/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/snapaligner/index/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/snapaligner/index/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/snapaligner/index/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/strobealign/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/strobealign/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/strobealign/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/strobealign/main.nf -------------------------------------------------------------------------------- /modules/nf-core/strobealign/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/strobealign/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/strobealign/strobealign.diff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/strobealign/strobealign.diff -------------------------------------------------------------------------------- /modules/nf-core/strobealign/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/strobealign/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/strobealign/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/strobealign/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/strobealign/tests/nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/strobealign/tests/nextflow.config -------------------------------------------------------------------------------- /modules/nf-core/wisecondorx/convert/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/wisecondorx/convert/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/wisecondorx/convert/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/wisecondorx/convert/main.nf -------------------------------------------------------------------------------- /modules/nf-core/wisecondorx/convert/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/wisecondorx/convert/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/wisecondorx/convert/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/wisecondorx/convert/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/wisecondorx/convert/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/wisecondorx/convert/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/wisecondorx/newref/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/wisecondorx/newref/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/wisecondorx/newref/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/wisecondorx/newref/main.nf -------------------------------------------------------------------------------- /modules/nf-core/wisecondorx/newref/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/wisecondorx/newref/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/wisecondorx/newref/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/wisecondorx/newref/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/wisecondorx/newref/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/wisecondorx/newref/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/wisecondorx/newref/tests/nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/wisecondorx/newref/tests/nextflow.config -------------------------------------------------------------------------------- /modules/nf-core/wisecondorx/predict/environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/wisecondorx/predict/environment.yml -------------------------------------------------------------------------------- /modules/nf-core/wisecondorx/predict/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/wisecondorx/predict/main.nf -------------------------------------------------------------------------------- /modules/nf-core/wisecondorx/predict/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/wisecondorx/predict/meta.yml -------------------------------------------------------------------------------- /modules/nf-core/wisecondorx/predict/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/wisecondorx/predict/tests/main.nf.test -------------------------------------------------------------------------------- /modules/nf-core/wisecondorx/predict/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/wisecondorx/predict/tests/main.nf.test.snap -------------------------------------------------------------------------------- /modules/nf-core/wisecondorx/predict/wisecondorx-predict.diff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/modules/nf-core/wisecondorx/predict/wisecondorx-predict.diff -------------------------------------------------------------------------------- /nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/nextflow.config -------------------------------------------------------------------------------- /nextflow_schema.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/nextflow_schema.json -------------------------------------------------------------------------------- /nf-test.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/nf-test.config -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/pyproject.toml -------------------------------------------------------------------------------- /subworkflows/local/build_pon/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/local/build_pon/main.nf -------------------------------------------------------------------------------- /subworkflows/local/build_pon/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/local/build_pon/meta.yml -------------------------------------------------------------------------------- /subworkflows/local/ichorcna/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/local/ichorcna/main.nf -------------------------------------------------------------------------------- /subworkflows/local/liquid_biopsy/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/local/liquid_biopsy/main.nf -------------------------------------------------------------------------------- /subworkflows/local/run_gistic/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/local/run_gistic/main.nf -------------------------------------------------------------------------------- /subworkflows/local/size_selection/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/local/size_selection/main.nf -------------------------------------------------------------------------------- /subworkflows/local/solid_biopsy/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/local/solid_biopsy/main.nf -------------------------------------------------------------------------------- /subworkflows/local/utils_samurai_pipeline/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/local/utils_samurai_pipeline/main.nf -------------------------------------------------------------------------------- /subworkflows/nf-core/bam_cnv_wisecondorx/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/bam_cnv_wisecondorx/main.nf -------------------------------------------------------------------------------- /subworkflows/nf-core/bam_cnv_wisecondorx/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/bam_cnv_wisecondorx/meta.yml -------------------------------------------------------------------------------- /subworkflows/nf-core/bam_cnv_wisecondorx/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/bam_cnv_wisecondorx/tests/main.nf.test -------------------------------------------------------------------------------- /subworkflows/nf-core/bam_cnv_wisecondorx/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/bam_cnv_wisecondorx/tests/main.nf.test.snap -------------------------------------------------------------------------------- /subworkflows/nf-core/bam_markduplicates_picard/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/bam_markduplicates_picard/main.nf -------------------------------------------------------------------------------- /subworkflows/nf-core/bam_markduplicates_picard/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/bam_markduplicates_picard/meta.yml -------------------------------------------------------------------------------- /subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test -------------------------------------------------------------------------------- /subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap -------------------------------------------------------------------------------- /subworkflows/nf-core/bam_qc_picard/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/bam_qc_picard/main.nf -------------------------------------------------------------------------------- /subworkflows/nf-core/bam_qc_picard/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/bam_qc_picard/meta.yml -------------------------------------------------------------------------------- /subworkflows/nf-core/bam_qc_picard/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/bam_qc_picard/tests/main.nf.test -------------------------------------------------------------------------------- /subworkflows/nf-core/bam_qc_picard/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/bam_qc_picard/tests/main.nf.test.snap -------------------------------------------------------------------------------- /subworkflows/nf-core/bam_sort_stats_samtools/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/bam_sort_stats_samtools/main.nf -------------------------------------------------------------------------------- /subworkflows/nf-core/bam_sort_stats_samtools/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/bam_sort_stats_samtools/meta.yml -------------------------------------------------------------------------------- /subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test -------------------------------------------------------------------------------- /subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap -------------------------------------------------------------------------------- /subworkflows/nf-core/bam_stats_samtools/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/bam_stats_samtools/main.nf -------------------------------------------------------------------------------- /subworkflows/nf-core/bam_stats_samtools/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/bam_stats_samtools/meta.yml -------------------------------------------------------------------------------- /subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test -------------------------------------------------------------------------------- /subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap -------------------------------------------------------------------------------- /subworkflows/nf-core/fasta_index_dna/fasta_index_dna.diff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/fasta_index_dna/fasta_index_dna.diff -------------------------------------------------------------------------------- /subworkflows/nf-core/fasta_index_dna/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/fasta_index_dna/main.nf -------------------------------------------------------------------------------- /subworkflows/nf-core/fasta_index_dna/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/fasta_index_dna/meta.yml -------------------------------------------------------------------------------- /subworkflows/nf-core/fastq_align_bwa/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/fastq_align_bwa/main.nf -------------------------------------------------------------------------------- /subworkflows/nf-core/fastq_align_bwa/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/fastq_align_bwa/meta.yml -------------------------------------------------------------------------------- /subworkflows/nf-core/fastq_align_bwa/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/fastq_align_bwa/tests/main.nf.test -------------------------------------------------------------------------------- /subworkflows/nf-core/fastq_align_bwa/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/fastq_align_bwa/tests/main.nf.test.snap -------------------------------------------------------------------------------- /subworkflows/nf-core/fastq_align_bwa/tests/nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/fastq_align_bwa/tests/nextflow.config -------------------------------------------------------------------------------- /subworkflows/nf-core/fastq_align_dna/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/fastq_align_dna/main.nf -------------------------------------------------------------------------------- /subworkflows/nf-core/fastq_align_dna/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/fastq_align_dna/meta.yml -------------------------------------------------------------------------------- /subworkflows/nf-core/fastq_align_dna/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/fastq_align_dna/tests/main.nf.test -------------------------------------------------------------------------------- /subworkflows/nf-core/fastq_align_dna/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/fastq_align_dna/tests/main.nf.test.snap -------------------------------------------------------------------------------- /subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf -------------------------------------------------------------------------------- /subworkflows/nf-core/fastq_trim_fastp_fastqc/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/fastq_trim_fastp_fastqc/meta.yml -------------------------------------------------------------------------------- /subworkflows/nf-core/fastq_trim_fastp_fastqc/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/fastq_trim_fastp_fastqc/tests/main.nf.test -------------------------------------------------------------------------------- /subworkflows/nf-core/fastq_trim_fastp_fastqc/tests/main.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/fastq_trim_fastp_fastqc/tests/main.nf.test.snap -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nextflow_pipeline/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/utils_nextflow_pipeline/main.nf -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nextflow_pipeline/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nfcore_pipeline/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/utils_nfcore_pipeline/main.nf -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nfcore_pipeline/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nfschema_plugin/main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/utils_nfschema_plugin/main.nf -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nfschema_plugin/meta.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/utils_nfschema_plugin/meta.yml -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config -------------------------------------------------------------------------------- /subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json -------------------------------------------------------------------------------- /tests/nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/tests/nextflow.config -------------------------------------------------------------------------------- /workflows/samurai.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DIncalciLab/samurai/HEAD/workflows/samurai.nf --------------------------------------------------------------------------------