├── .gitattributes ├── .github ├── .dockstore.yml ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE │ ├── bug_report.yml │ ├── config.yml │ └── feature_request.yml ├── PULL_REQUEST_TEMPLATE.md └── workflows │ ├── awsfulltest.yml │ ├── awstest.yml │ ├── branch.yml │ ├── ci.yml │ ├── linting.yml │ └── linting_comment.yml ├── .gitignore ├── .markdownlint.yml ├── .nf-core.yml ├── .readthedocs.yaml ├── CHANGELOG.md ├── CITATIONS.md ├── CODE_OF_CONDUCT.md ├── Dockerfile ├── LICENSE ├── README.md ├── assets ├── demo │ ├── CORG-X1.fastq.gz │ ├── CORG-X2.fastq.gz │ ├── CORG-Y1.fastq.gz │ ├── CORG-Z1.fastq.gz │ ├── SRA_IDs.txt │ ├── SRAannots2CV.txt │ ├── UnitTest │ │ └── SRA_IDs.txt │ ├── references │ │ ├── COMMANDS.sh │ │ ├── CORG.fna │ │ ├── CORG.genome.Hisat2.indexed │ │ │ ├── CORG.1.ht2 │ │ │ ├── CORG.2.ht2 │ │ │ ├── CORG.3.ht2 │ │ │ ├── CORG.4.ht2 │ │ │ ├── CORG.5.ht2 │ │ │ ├── CORG.6.ht2 │ │ │ ├── CORG.7.ht2 │ │ │ └── CORG.8.ht2 │ │ ├── CORG.genome.Star.indexed │ │ │ ├── Genome │ │ │ ├── Log.out │ │ │ ├── SA │ │ │ ├── SAindex │ │ │ ├── chrLength.txt │ │ │ ├── chrName.txt │ │ │ ├── chrNameLength.txt │ │ │ ├── chrStart.txt │ │ │ ├── exonGeTrInfo.tab │ │ │ ├── exonInfo.tab │ │ │ ├── geneInfo.tab │ │ │ ├── genomeParameters.txt │ │ │ ├── sjdbInfo.txt │ │ │ ├── sjdbList.fromGTF.out.tab │ │ │ ├── sjdbList.out.tab │ │ │ └── transcriptInfo.tab │ │ ├── CORG.transcripts │ │ ├── CORG.transcripts.Kallisto.indexed │ │ ├── CORG.transcripts.Salmon.indexed │ │ │ ├── complete_ref_lens.bin │ │ │ ├── ctable.bin │ │ │ ├── ctg_offsets.bin │ │ │ ├── duplicate_clusters.tsv │ │ │ ├── hash.bin │ │ │ ├── header.json │ │ │ ├── indexing.log │ │ │ ├── info.json │ │ │ ├── mphf.bin │ │ │ ├── pos.bin │ │ │ ├── pre_indexing.log │ │ │ ├── quasi_index.log │ │ │ ├── rank.bin │ │ │ ├── refAccumLengths.bin │ │ │ ├── refInfo.json │ │ │ ├── ref_indexing.log │ │ │ ├── reflengths.bin │ │ │ ├── refseq.bin │ │ │ ├── rsd.bin │ │ │ ├── sa.bin │ │ │ ├── seq.bin │ │ │ ├── txpInfo.bin │ │ │ └── versionInfo.json │ │ ├── CORG.transcripts.clean │ │ ├── CORG.transcripts.gtf │ │ ├── CORG.transcripts.tlst │ │ └── hisat2-build.log │ └── samples2skip.txt ├── email_template.html ├── email_template.txt ├── failed_sra_runs.template.html ├── fasta_adapter.txt ├── multiqc_config.yaml ├── nf-systemsgenetics-gemmaker_logo.png └── sendmail_template.txt ├── bin ├── clean_work_files.sh ├── create-gem.py ├── create_SRA_amx.py ├── failed_runs_report.py ├── markdown_to_html.py ├── merge_fastq.py ├── retrieve_sra.py ├── retrieve_sra_metadata.py ├── retrieve_sra_spots.py ├── scrape_software_versions.py ├── split-sra-ids.py ├── sra2fastq.py └── sra_meta2biosample.py ├── conf ├── base.config ├── igenomes.config ├── modules.config ├── test.config ├── test_full.config └── test_noclean.config ├── docs ├── Makefile ├── README.md ├── SRA_IDs.txt ├── citations.rst ├── conf.py ├── execution.rst ├── explore.rst ├── images │ ├── GEMmaker-logo-sm.png │ ├── GEMmaker-logo.png │ ├── MultiQC_Report.png │ ├── NSF.png │ ├── SciDAS.png │ ├── Timeline.png │ ├── WSU.png │ ├── clemson.png │ ├── ease_of_use.png │ ├── failed_runs_report.png │ ├── findable_data.png │ ├── flowchartgen.png │ ├── heatmap.png │ ├── interoperable.png │ ├── nextflow_report.png │ ├── nextflow_timeline.png │ ├── nf-systemsgenetics-gemmaker_logo.png │ ├── renci.png │ ├── reproducible.png │ └── scalable.png ├── index.rst ├── installation.rst ├── make.bat ├── output.md ├── prepare_reference.rst ├── prepare_samples.rst ├── requirements.txt ├── results.rst ├── troubleshooting.rst ├── usage.md └── whats_next.rst ├── environment.yml ├── lib ├── NfcoreSchema.groovy ├── NfcoreTemplate.groovy ├── Utils.groovy ├── WorkflowGEMmaker.groovy ├── WorkflowMain.groovy └── nfcore_external_java_deps.jar ├── main.nf ├── modules.json ├── modules └── local │ ├── clean_work_dirs.nf │ ├── clean_work_files.nf │ ├── create_gem.nf │ ├── download_runs.nf │ ├── failed_run_report.nf │ ├── fastq_dump.nf │ ├── fastq_merge.nf │ ├── fastqc.nf │ ├── functions.nf │ ├── get_software_versions.nf │ ├── hisat2.nf │ ├── kallisto.nf │ ├── kallisto_tpm.nf │ ├── multiqc.nf │ ├── next_sample.nf │ ├── retrieve_sra_metadata.nf │ ├── salmon.nf │ ├── salmon_tpm.nf │ ├── samtools_index.nf │ ├── samtools_merge.nf │ ├── samtools_sort.nf │ ├── star.nf │ ├── stringtie.nf │ ├── stringtie_fpkm_tpm.nf │ └── trimmomatic.nf ├── nextflow.config ├── nextflow_schema.json └── workflows └── GEMmaker.nf /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/.gitattributes -------------------------------------------------------------------------------- /.github/.dockstore.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/.github/.dockstore.yml -------------------------------------------------------------------------------- /.github/CONTRIBUTING.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/.github/CONTRIBUTING.md -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/bug_report.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/.github/ISSUE_TEMPLATE/bug_report.yml -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/config.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/.github/ISSUE_TEMPLATE/config.yml -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/feature_request.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/.github/ISSUE_TEMPLATE/feature_request.yml -------------------------------------------------------------------------------- /.github/PULL_REQUEST_TEMPLATE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/.github/PULL_REQUEST_TEMPLATE.md -------------------------------------------------------------------------------- /.github/workflows/awsfulltest.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/.github/workflows/awsfulltest.yml -------------------------------------------------------------------------------- /.github/workflows/awstest.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/.github/workflows/awstest.yml -------------------------------------------------------------------------------- /.github/workflows/branch.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/.github/workflows/branch.yml -------------------------------------------------------------------------------- /.github/workflows/ci.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/.github/workflows/ci.yml -------------------------------------------------------------------------------- /.github/workflows/linting.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/.github/workflows/linting.yml -------------------------------------------------------------------------------- /.github/workflows/linting_comment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/.github/workflows/linting_comment.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/.gitignore -------------------------------------------------------------------------------- /.markdownlint.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/.markdownlint.yml -------------------------------------------------------------------------------- /.nf-core.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/.nf-core.yml -------------------------------------------------------------------------------- /.readthedocs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/.readthedocs.yaml -------------------------------------------------------------------------------- /CHANGELOG.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/CHANGELOG.md -------------------------------------------------------------------------------- /CITATIONS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/CITATIONS.md -------------------------------------------------------------------------------- /CODE_OF_CONDUCT.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/CODE_OF_CONDUCT.md -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/Dockerfile -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/README.md -------------------------------------------------------------------------------- /assets/demo/CORG-X1.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/CORG-X1.fastq.gz -------------------------------------------------------------------------------- /assets/demo/CORG-X2.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/CORG-X2.fastq.gz -------------------------------------------------------------------------------- /assets/demo/CORG-Y1.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/CORG-Y1.fastq.gz -------------------------------------------------------------------------------- /assets/demo/CORG-Z1.fastq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/CORG-Z1.fastq.gz -------------------------------------------------------------------------------- /assets/demo/SRA_IDs.txt: -------------------------------------------------------------------------------- 1 | SRR649944 2 | -------------------------------------------------------------------------------- /assets/demo/SRAannots2CV.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/SRAannots2CV.txt -------------------------------------------------------------------------------- /assets/demo/UnitTest/SRA_IDs.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/UnitTest/SRA_IDs.txt -------------------------------------------------------------------------------- /assets/demo/references/COMMANDS.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/COMMANDS.sh -------------------------------------------------------------------------------- /assets/demo/references/CORG.fna: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.fna -------------------------------------------------------------------------------- /assets/demo/references/CORG.genome.Hisat2.indexed/CORG.1.ht2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.genome.Hisat2.indexed/CORG.1.ht2 -------------------------------------------------------------------------------- /assets/demo/references/CORG.genome.Hisat2.indexed/CORG.2.ht2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.genome.Hisat2.indexed/CORG.2.ht2 -------------------------------------------------------------------------------- /assets/demo/references/CORG.genome.Hisat2.indexed/CORG.3.ht2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.genome.Hisat2.indexed/CORG.3.ht2 -------------------------------------------------------------------------------- /assets/demo/references/CORG.genome.Hisat2.indexed/CORG.4.ht2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.genome.Hisat2.indexed/CORG.4.ht2 -------------------------------------------------------------------------------- /assets/demo/references/CORG.genome.Hisat2.indexed/CORG.5.ht2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.genome.Hisat2.indexed/CORG.5.ht2 -------------------------------------------------------------------------------- /assets/demo/references/CORG.genome.Hisat2.indexed/CORG.6.ht2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.genome.Hisat2.indexed/CORG.6.ht2 -------------------------------------------------------------------------------- /assets/demo/references/CORG.genome.Hisat2.indexed/CORG.7.ht2: -------------------------------------------------------------------------------- 1 | cd@ -------------------------------------------------------------------------------- /assets/demo/references/CORG.genome.Hisat2.indexed/CORG.8.ht2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.genome.Hisat2.indexed/CORG.8.ht2 -------------------------------------------------------------------------------- /assets/demo/references/CORG.genome.Star.indexed/Genome: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.genome.Star.indexed/Genome -------------------------------------------------------------------------------- /assets/demo/references/CORG.genome.Star.indexed/Log.out: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.genome.Star.indexed/Log.out -------------------------------------------------------------------------------- /assets/demo/references/CORG.genome.Star.indexed/SA: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.genome.Star.indexed/SA -------------------------------------------------------------------------------- /assets/demo/references/CORG.genome.Star.indexed/SAindex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.genome.Star.indexed/SAindex -------------------------------------------------------------------------------- /assets/demo/references/CORG.genome.Star.indexed/chrLength.txt: -------------------------------------------------------------------------------- 1 | 1120 2 | 833 3 | 350 4 | -------------------------------------------------------------------------------- /assets/demo/references/CORG.genome.Star.indexed/chrName.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.genome.Star.indexed/chrName.txt -------------------------------------------------------------------------------- /assets/demo/references/CORG.genome.Star.indexed/chrNameLength.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.genome.Star.indexed/chrNameLength.txt -------------------------------------------------------------------------------- /assets/demo/references/CORG.genome.Star.indexed/chrStart.txt: -------------------------------------------------------------------------------- 1 | 0 2 | 262144 3 | 524288 4 | 786432 5 | -------------------------------------------------------------------------------- /assets/demo/references/CORG.genome.Star.indexed/exonGeTrInfo.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.genome.Star.indexed/exonGeTrInfo.tab -------------------------------------------------------------------------------- /assets/demo/references/CORG.genome.Star.indexed/exonInfo.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.genome.Star.indexed/exonInfo.tab -------------------------------------------------------------------------------- /assets/demo/references/CORG.genome.Star.indexed/geneInfo.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.genome.Star.indexed/geneInfo.tab -------------------------------------------------------------------------------- /assets/demo/references/CORG.genome.Star.indexed/genomeParameters.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.genome.Star.indexed/genomeParameters.txt -------------------------------------------------------------------------------- /assets/demo/references/CORG.genome.Star.indexed/sjdbInfo.txt: -------------------------------------------------------------------------------- 1 | 0 100 2 | -------------------------------------------------------------------------------- /assets/demo/references/CORG.genome.Star.indexed/sjdbList.fromGTF.out.tab: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /assets/demo/references/CORG.genome.Star.indexed/sjdbList.out.tab: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /assets/demo/references/CORG.genome.Star.indexed/transcriptInfo.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.genome.Star.indexed/transcriptInfo.tab -------------------------------------------------------------------------------- /assets/demo/references/CORG.transcripts: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.transcripts -------------------------------------------------------------------------------- /assets/demo/references/CORG.transcripts.Kallisto.indexed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.transcripts.Kallisto.indexed -------------------------------------------------------------------------------- /assets/demo/references/CORG.transcripts.Salmon.indexed/complete_ref_lens.bin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.transcripts.Salmon.indexed/complete_ref_lens.bin -------------------------------------------------------------------------------- /assets/demo/references/CORG.transcripts.Salmon.indexed/ctable.bin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.transcripts.Salmon.indexed/ctable.bin -------------------------------------------------------------------------------- /assets/demo/references/CORG.transcripts.Salmon.indexed/ctg_offsets.bin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.transcripts.Salmon.indexed/ctg_offsets.bin -------------------------------------------------------------------------------- /assets/demo/references/CORG.transcripts.Salmon.indexed/duplicate_clusters.tsv: -------------------------------------------------------------------------------- 1 | RetainedRef DuplicateRef 2 | -------------------------------------------------------------------------------- /assets/demo/references/CORG.transcripts.Salmon.indexed/hash.bin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.transcripts.Salmon.indexed/hash.bin -------------------------------------------------------------------------------- /assets/demo/references/CORG.transcripts.Salmon.indexed/header.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.transcripts.Salmon.indexed/header.json -------------------------------------------------------------------------------- /assets/demo/references/CORG.transcripts.Salmon.indexed/indexing.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.transcripts.Salmon.indexed/indexing.log -------------------------------------------------------------------------------- /assets/demo/references/CORG.transcripts.Salmon.indexed/info.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.transcripts.Salmon.indexed/info.json -------------------------------------------------------------------------------- /assets/demo/references/CORG.transcripts.Salmon.indexed/mphf.bin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.transcripts.Salmon.indexed/mphf.bin -------------------------------------------------------------------------------- /assets/demo/references/CORG.transcripts.Salmon.indexed/pos.bin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.transcripts.Salmon.indexed/pos.bin -------------------------------------------------------------------------------- /assets/demo/references/CORG.transcripts.Salmon.indexed/pre_indexing.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.transcripts.Salmon.indexed/pre_indexing.log -------------------------------------------------------------------------------- /assets/demo/references/CORG.transcripts.Salmon.indexed/quasi_index.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.transcripts.Salmon.indexed/quasi_index.log -------------------------------------------------------------------------------- /assets/demo/references/CORG.transcripts.Salmon.indexed/rank.bin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.transcripts.Salmon.indexed/rank.bin -------------------------------------------------------------------------------- /assets/demo/references/CORG.transcripts.Salmon.indexed/refAccumLengths.bin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.transcripts.Salmon.indexed/refAccumLengths.bin -------------------------------------------------------------------------------- /assets/demo/references/CORG.transcripts.Salmon.indexed/refInfo.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.transcripts.Salmon.indexed/refInfo.json -------------------------------------------------------------------------------- /assets/demo/references/CORG.transcripts.Salmon.indexed/ref_indexing.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.transcripts.Salmon.indexed/ref_indexing.log -------------------------------------------------------------------------------- /assets/demo/references/CORG.transcripts.Salmon.indexed/reflengths.bin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.transcripts.Salmon.indexed/reflengths.bin -------------------------------------------------------------------------------- /assets/demo/references/CORG.transcripts.Salmon.indexed/refseq.bin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.transcripts.Salmon.indexed/refseq.bin -------------------------------------------------------------------------------- /assets/demo/references/CORG.transcripts.Salmon.indexed/rsd.bin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.transcripts.Salmon.indexed/rsd.bin -------------------------------------------------------------------------------- /assets/demo/references/CORG.transcripts.Salmon.indexed/sa.bin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.transcripts.Salmon.indexed/sa.bin -------------------------------------------------------------------------------- /assets/demo/references/CORG.transcripts.Salmon.indexed/seq.bin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.transcripts.Salmon.indexed/seq.bin -------------------------------------------------------------------------------- /assets/demo/references/CORG.transcripts.Salmon.indexed/txpInfo.bin: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.transcripts.Salmon.indexed/txpInfo.bin -------------------------------------------------------------------------------- /assets/demo/references/CORG.transcripts.Salmon.indexed/versionInfo.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.transcripts.Salmon.indexed/versionInfo.json -------------------------------------------------------------------------------- /assets/demo/references/CORG.transcripts.clean: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.transcripts.clean -------------------------------------------------------------------------------- /assets/demo/references/CORG.transcripts.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.transcripts.gtf -------------------------------------------------------------------------------- /assets/demo/references/CORG.transcripts.tlst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/CORG.transcripts.tlst -------------------------------------------------------------------------------- /assets/demo/references/hisat2-build.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/demo/references/hisat2-build.log -------------------------------------------------------------------------------- /assets/demo/samples2skip.txt: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /assets/email_template.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/email_template.html -------------------------------------------------------------------------------- /assets/email_template.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/email_template.txt -------------------------------------------------------------------------------- /assets/failed_sra_runs.template.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/failed_sra_runs.template.html -------------------------------------------------------------------------------- /assets/fasta_adapter.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/fasta_adapter.txt -------------------------------------------------------------------------------- /assets/multiqc_config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/multiqc_config.yaml -------------------------------------------------------------------------------- /assets/nf-systemsgenetics-gemmaker_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/nf-systemsgenetics-gemmaker_logo.png -------------------------------------------------------------------------------- /assets/sendmail_template.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/assets/sendmail_template.txt -------------------------------------------------------------------------------- /bin/clean_work_files.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/bin/clean_work_files.sh -------------------------------------------------------------------------------- /bin/create-gem.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/bin/create-gem.py -------------------------------------------------------------------------------- /bin/create_SRA_amx.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/bin/create_SRA_amx.py -------------------------------------------------------------------------------- /bin/failed_runs_report.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/bin/failed_runs_report.py -------------------------------------------------------------------------------- /bin/markdown_to_html.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/bin/markdown_to_html.py -------------------------------------------------------------------------------- /bin/merge_fastq.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/bin/merge_fastq.py -------------------------------------------------------------------------------- /bin/retrieve_sra.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/bin/retrieve_sra.py -------------------------------------------------------------------------------- /bin/retrieve_sra_metadata.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/bin/retrieve_sra_metadata.py -------------------------------------------------------------------------------- /bin/retrieve_sra_spots.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/bin/retrieve_sra_spots.py -------------------------------------------------------------------------------- /bin/scrape_software_versions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/bin/scrape_software_versions.py -------------------------------------------------------------------------------- /bin/split-sra-ids.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/bin/split-sra-ids.py -------------------------------------------------------------------------------- /bin/sra2fastq.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/bin/sra2fastq.py -------------------------------------------------------------------------------- /bin/sra_meta2biosample.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/bin/sra_meta2biosample.py -------------------------------------------------------------------------------- /conf/base.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/conf/base.config -------------------------------------------------------------------------------- /conf/igenomes.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/conf/igenomes.config -------------------------------------------------------------------------------- /conf/modules.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/conf/modules.config -------------------------------------------------------------------------------- /conf/test.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/conf/test.config -------------------------------------------------------------------------------- /conf/test_full.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/conf/test_full.config -------------------------------------------------------------------------------- /conf/test_noclean.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/conf/test_noclean.config -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/Makefile -------------------------------------------------------------------------------- /docs/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/README.md -------------------------------------------------------------------------------- /docs/SRA_IDs.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/SRA_IDs.txt -------------------------------------------------------------------------------- /docs/citations.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/citations.rst -------------------------------------------------------------------------------- /docs/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/conf.py -------------------------------------------------------------------------------- /docs/execution.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/execution.rst -------------------------------------------------------------------------------- /docs/explore.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/explore.rst -------------------------------------------------------------------------------- /docs/images/GEMmaker-logo-sm.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/images/GEMmaker-logo-sm.png -------------------------------------------------------------------------------- /docs/images/GEMmaker-logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/images/GEMmaker-logo.png -------------------------------------------------------------------------------- /docs/images/MultiQC_Report.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/images/MultiQC_Report.png -------------------------------------------------------------------------------- /docs/images/NSF.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/images/NSF.png -------------------------------------------------------------------------------- /docs/images/SciDAS.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/images/SciDAS.png -------------------------------------------------------------------------------- /docs/images/Timeline.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/images/Timeline.png -------------------------------------------------------------------------------- /docs/images/WSU.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/images/WSU.png -------------------------------------------------------------------------------- /docs/images/clemson.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/images/clemson.png -------------------------------------------------------------------------------- /docs/images/ease_of_use.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/images/ease_of_use.png -------------------------------------------------------------------------------- /docs/images/failed_runs_report.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/images/failed_runs_report.png -------------------------------------------------------------------------------- /docs/images/findable_data.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/images/findable_data.png -------------------------------------------------------------------------------- /docs/images/flowchartgen.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/images/flowchartgen.png -------------------------------------------------------------------------------- /docs/images/heatmap.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/images/heatmap.png -------------------------------------------------------------------------------- /docs/images/interoperable.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/images/interoperable.png -------------------------------------------------------------------------------- /docs/images/nextflow_report.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/images/nextflow_report.png -------------------------------------------------------------------------------- /docs/images/nextflow_timeline.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/images/nextflow_timeline.png -------------------------------------------------------------------------------- /docs/images/nf-systemsgenetics-gemmaker_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/images/nf-systemsgenetics-gemmaker_logo.png -------------------------------------------------------------------------------- /docs/images/renci.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/images/renci.png -------------------------------------------------------------------------------- /docs/images/reproducible.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/images/reproducible.png -------------------------------------------------------------------------------- /docs/images/scalable.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/images/scalable.png -------------------------------------------------------------------------------- /docs/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/index.rst -------------------------------------------------------------------------------- /docs/installation.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/installation.rst -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/make.bat -------------------------------------------------------------------------------- /docs/output.md: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /docs/prepare_reference.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/prepare_reference.rst -------------------------------------------------------------------------------- /docs/prepare_samples.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/prepare_samples.rst -------------------------------------------------------------------------------- /docs/requirements.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /docs/results.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/results.rst -------------------------------------------------------------------------------- /docs/troubleshooting.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/troubleshooting.rst -------------------------------------------------------------------------------- /docs/usage.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/usage.md -------------------------------------------------------------------------------- /docs/whats_next.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/docs/whats_next.rst -------------------------------------------------------------------------------- /environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/environment.yml -------------------------------------------------------------------------------- /lib/NfcoreSchema.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/lib/NfcoreSchema.groovy -------------------------------------------------------------------------------- /lib/NfcoreTemplate.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/lib/NfcoreTemplate.groovy -------------------------------------------------------------------------------- /lib/Utils.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/lib/Utils.groovy -------------------------------------------------------------------------------- /lib/WorkflowGEMmaker.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/lib/WorkflowGEMmaker.groovy -------------------------------------------------------------------------------- /lib/WorkflowMain.groovy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/lib/WorkflowMain.groovy -------------------------------------------------------------------------------- /lib/nfcore_external_java_deps.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/lib/nfcore_external_java_deps.jar -------------------------------------------------------------------------------- /main.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/main.nf -------------------------------------------------------------------------------- /modules.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/modules.json -------------------------------------------------------------------------------- /modules/local/clean_work_dirs.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/modules/local/clean_work_dirs.nf -------------------------------------------------------------------------------- /modules/local/clean_work_files.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/modules/local/clean_work_files.nf -------------------------------------------------------------------------------- /modules/local/create_gem.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/modules/local/create_gem.nf -------------------------------------------------------------------------------- /modules/local/download_runs.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/modules/local/download_runs.nf -------------------------------------------------------------------------------- /modules/local/failed_run_report.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/modules/local/failed_run_report.nf -------------------------------------------------------------------------------- /modules/local/fastq_dump.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/modules/local/fastq_dump.nf -------------------------------------------------------------------------------- /modules/local/fastq_merge.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/modules/local/fastq_merge.nf -------------------------------------------------------------------------------- /modules/local/fastqc.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/modules/local/fastqc.nf -------------------------------------------------------------------------------- /modules/local/functions.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/modules/local/functions.nf -------------------------------------------------------------------------------- /modules/local/get_software_versions.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/modules/local/get_software_versions.nf -------------------------------------------------------------------------------- /modules/local/hisat2.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/modules/local/hisat2.nf -------------------------------------------------------------------------------- /modules/local/kallisto.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/modules/local/kallisto.nf -------------------------------------------------------------------------------- /modules/local/kallisto_tpm.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/modules/local/kallisto_tpm.nf -------------------------------------------------------------------------------- /modules/local/multiqc.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/modules/local/multiqc.nf -------------------------------------------------------------------------------- /modules/local/next_sample.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/modules/local/next_sample.nf -------------------------------------------------------------------------------- /modules/local/retrieve_sra_metadata.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/modules/local/retrieve_sra_metadata.nf -------------------------------------------------------------------------------- /modules/local/salmon.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/modules/local/salmon.nf -------------------------------------------------------------------------------- /modules/local/salmon_tpm.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/modules/local/salmon_tpm.nf -------------------------------------------------------------------------------- /modules/local/samtools_index.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/modules/local/samtools_index.nf -------------------------------------------------------------------------------- /modules/local/samtools_merge.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/modules/local/samtools_merge.nf -------------------------------------------------------------------------------- /modules/local/samtools_sort.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/modules/local/samtools_sort.nf -------------------------------------------------------------------------------- /modules/local/star.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/modules/local/star.nf -------------------------------------------------------------------------------- /modules/local/stringtie.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/modules/local/stringtie.nf -------------------------------------------------------------------------------- /modules/local/stringtie_fpkm_tpm.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/modules/local/stringtie_fpkm_tpm.nf -------------------------------------------------------------------------------- /modules/local/trimmomatic.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/modules/local/trimmomatic.nf -------------------------------------------------------------------------------- /nextflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/nextflow.config -------------------------------------------------------------------------------- /nextflow_schema.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/nextflow_schema.json -------------------------------------------------------------------------------- /workflows/GEMmaker.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SystemsGenetics/GEMmaker/HEAD/workflows/GEMmaker.nf --------------------------------------------------------------------------------