├── .gitignore ├── .gitmodules ├── .travis.yml ├── CHANGELOG.md ├── CONTRIBUTING.md ├── README.md ├── alces-flight ├── README.md └── clusterflow.config ├── cf ├── clusterflow.config.example ├── docs ├── README.md ├── assets │ ├── CF_mini.gif │ ├── Cluster_Flow_logo.ai │ ├── Cluster_Flow_logo.png │ ├── example_report_bad.html │ ├── example_report_good.html │ ├── example_report_highlights.html │ └── example_report_warnings.html ├── command_line.md ├── configuration.md ├── installation.md ├── module_options.md ├── modules.md ├── pipelines.md ├── troubleshooting.md └── usage.md ├── genomes.config.example ├── genomes.d └── example.config.template ├── license.txt ├── modules ├── CF ├── bedToNrf.cfmod.pl ├── bedtools_bamToBed.cfmod.pl ├── bedtools_intersectNeg.cfmod.pl ├── bismark_align.cfmod.pl ├── bismark_deduplicate.cfmod.pl ├── bismark_methXtract.cfmod.pl ├── bismark_report.cfmod.pl ├── bismark_summary_report.cfmod.pl ├── bowtie.cfmod.pl ├── bowtie1.cfmod.pl ├── bowtie2.cfmod.pl ├── bwa.cfmod.pl ├── cf_download.cfmod.pl ├── cf_merge_files.cfmod.pl ├── cf_run_finished.cfmod.pl ├── cf_runs_all_finished.cfmod.pl ├── deeptools_bamCoverage.cfmod.pl ├── deeptools_bamFingerprint.cfmod.pl ├── example_module.R ├── example_module.pl ├── fastq_screen.cfmod.pl ├── fastqc.cfmod.pl ├── featureCounts.cfmod.pl ├── hicup.cfmod.pl ├── hisat2.cfmod.pl ├── htseq_counts.cfmod.pl ├── kallisto.cfmod.pl ├── multiqc.cfmod.pl ├── phantompeaktools_runSpp.cfmod.pl ├── picard_dedup.cfmod.pl ├── preseq_calc.cfmod.pl ├── rseqc_geneBody_coverage.cfmod.pl ├── rseqc_inner_distance.cfmod.pl ├── rseqc_junctions.cfmod.pl ├── rseqc_read_GC.cfmod.pl ├── salmon.cfmod.pl ├── samtools_bam2sam.cfmod.pl ├── samtools_dedup.cfmod.pl ├── samtools_sort_index.cfmod.pl ├── sra_abidump.cfmod.pl ├── sra_fqdump.cfmod.pl ├── star.cfmod.pl ├── tophat.cfmod.pl ├── tophat_broken_MAPQ.cfmod.pl └── trim_galore.cfmod.pl ├── pipelines ├── bam_preseq.config ├── bismark.config ├── bismark_RRBS.config ├── bismark_pbat.config ├── bismark_singlecell.config ├── bwa_preseq.config ├── chipseq_qc.config ├── fastq_bismark.config ├── fastq_bismark_RRBS.config ├── fastq_bowtie.config ├── fastq_bowtie1_miRNA.config ├── fastq_hicup.config ├── fastq_hisat2.config ├── fastq_pbat.config ├── fastq_salmon.config ├── fastq_star.config ├── fastq_tophat.config ├── sra_bismark.config ├── sra_bismark_RRBS.config ├── sra_bowtie.config ├── sra_bowtie1.config ├── sra_bowtie1_miRNA.config ├── sra_bowtie2.config ├── sra_hicup.config ├── sra_hisat2.config ├── sra_pbat.config ├── sra_tophat.config ├── sra_trim.config ├── trim_bowtie_miRNA.config └── trim_tophat.config └── source └── CF ├── Constants.pm ├── Headnodehelpers.pm ├── Helpers.pm ├── Helpers.py ├── __init__.py ├── cf_tests.pl ├── html_email_template.html └── plaintext_email_template.txt /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/.gitignore -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/.travis.yml -------------------------------------------------------------------------------- /CHANGELOG.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/CHANGELOG.md -------------------------------------------------------------------------------- /CONTRIBUTING.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/CONTRIBUTING.md -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/README.md -------------------------------------------------------------------------------- /alces-flight/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/alces-flight/README.md -------------------------------------------------------------------------------- /alces-flight/clusterflow.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/alces-flight/clusterflow.config -------------------------------------------------------------------------------- /cf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/cf -------------------------------------------------------------------------------- /clusterflow.config.example: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/clusterflow.config.example -------------------------------------------------------------------------------- /docs/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/docs/README.md -------------------------------------------------------------------------------- /docs/assets/CF_mini.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/docs/assets/CF_mini.gif -------------------------------------------------------------------------------- /docs/assets/Cluster_Flow_logo.ai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/docs/assets/Cluster_Flow_logo.ai -------------------------------------------------------------------------------- /docs/assets/Cluster_Flow_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/docs/assets/Cluster_Flow_logo.png -------------------------------------------------------------------------------- /docs/assets/example_report_bad.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/docs/assets/example_report_bad.html -------------------------------------------------------------------------------- /docs/assets/example_report_good.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/docs/assets/example_report_good.html -------------------------------------------------------------------------------- /docs/assets/example_report_highlights.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/docs/assets/example_report_highlights.html -------------------------------------------------------------------------------- /docs/assets/example_report_warnings.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/docs/assets/example_report_warnings.html -------------------------------------------------------------------------------- /docs/command_line.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/docs/command_line.md -------------------------------------------------------------------------------- /docs/configuration.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/docs/configuration.md -------------------------------------------------------------------------------- /docs/installation.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/docs/installation.md -------------------------------------------------------------------------------- /docs/module_options.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/docs/module_options.md -------------------------------------------------------------------------------- /docs/modules.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/docs/modules.md -------------------------------------------------------------------------------- /docs/pipelines.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/docs/pipelines.md -------------------------------------------------------------------------------- /docs/troubleshooting.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/docs/troubleshooting.md -------------------------------------------------------------------------------- /docs/usage.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/docs/usage.md -------------------------------------------------------------------------------- /genomes.config.example: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/genomes.config.example -------------------------------------------------------------------------------- /genomes.d/example.config.template: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/genomes.d/example.config.template -------------------------------------------------------------------------------- /license.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/license.txt -------------------------------------------------------------------------------- /modules/CF: -------------------------------------------------------------------------------- 1 | ../source/CF -------------------------------------------------------------------------------- /modules/bedToNrf.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/bedToNrf.cfmod.pl -------------------------------------------------------------------------------- /modules/bedtools_bamToBed.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/bedtools_bamToBed.cfmod.pl -------------------------------------------------------------------------------- /modules/bedtools_intersectNeg.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/bedtools_intersectNeg.cfmod.pl -------------------------------------------------------------------------------- /modules/bismark_align.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/bismark_align.cfmod.pl -------------------------------------------------------------------------------- /modules/bismark_deduplicate.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/bismark_deduplicate.cfmod.pl -------------------------------------------------------------------------------- /modules/bismark_methXtract.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/bismark_methXtract.cfmod.pl -------------------------------------------------------------------------------- /modules/bismark_report.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/bismark_report.cfmod.pl -------------------------------------------------------------------------------- /modules/bismark_summary_report.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/bismark_summary_report.cfmod.pl -------------------------------------------------------------------------------- /modules/bowtie.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/bowtie.cfmod.pl -------------------------------------------------------------------------------- /modules/bowtie1.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/bowtie1.cfmod.pl -------------------------------------------------------------------------------- /modules/bowtie2.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/bowtie2.cfmod.pl -------------------------------------------------------------------------------- /modules/bwa.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/bwa.cfmod.pl -------------------------------------------------------------------------------- /modules/cf_download.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/cf_download.cfmod.pl -------------------------------------------------------------------------------- /modules/cf_merge_files.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/cf_merge_files.cfmod.pl -------------------------------------------------------------------------------- /modules/cf_run_finished.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/cf_run_finished.cfmod.pl -------------------------------------------------------------------------------- /modules/cf_runs_all_finished.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/cf_runs_all_finished.cfmod.pl -------------------------------------------------------------------------------- /modules/deeptools_bamCoverage.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/deeptools_bamCoverage.cfmod.pl -------------------------------------------------------------------------------- /modules/deeptools_bamFingerprint.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/deeptools_bamFingerprint.cfmod.pl -------------------------------------------------------------------------------- /modules/example_module.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/example_module.R -------------------------------------------------------------------------------- /modules/example_module.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/example_module.pl -------------------------------------------------------------------------------- /modules/fastq_screen.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/fastq_screen.cfmod.pl -------------------------------------------------------------------------------- /modules/fastqc.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/fastqc.cfmod.pl -------------------------------------------------------------------------------- /modules/featureCounts.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/featureCounts.cfmod.pl -------------------------------------------------------------------------------- /modules/hicup.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/hicup.cfmod.pl -------------------------------------------------------------------------------- /modules/hisat2.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/hisat2.cfmod.pl -------------------------------------------------------------------------------- /modules/htseq_counts.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/htseq_counts.cfmod.pl -------------------------------------------------------------------------------- /modules/kallisto.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/kallisto.cfmod.pl -------------------------------------------------------------------------------- /modules/multiqc.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/multiqc.cfmod.pl -------------------------------------------------------------------------------- /modules/phantompeaktools_runSpp.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/phantompeaktools_runSpp.cfmod.pl -------------------------------------------------------------------------------- /modules/picard_dedup.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/picard_dedup.cfmod.pl -------------------------------------------------------------------------------- /modules/preseq_calc.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/preseq_calc.cfmod.pl -------------------------------------------------------------------------------- /modules/rseqc_geneBody_coverage.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/rseqc_geneBody_coverage.cfmod.pl -------------------------------------------------------------------------------- /modules/rseqc_inner_distance.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/rseqc_inner_distance.cfmod.pl -------------------------------------------------------------------------------- /modules/rseqc_junctions.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/rseqc_junctions.cfmod.pl -------------------------------------------------------------------------------- /modules/rseqc_read_GC.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/rseqc_read_GC.cfmod.pl -------------------------------------------------------------------------------- /modules/salmon.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/salmon.cfmod.pl -------------------------------------------------------------------------------- /modules/samtools_bam2sam.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/samtools_bam2sam.cfmod.pl -------------------------------------------------------------------------------- /modules/samtools_dedup.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/samtools_dedup.cfmod.pl -------------------------------------------------------------------------------- /modules/samtools_sort_index.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/samtools_sort_index.cfmod.pl -------------------------------------------------------------------------------- /modules/sra_abidump.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/sra_abidump.cfmod.pl -------------------------------------------------------------------------------- /modules/sra_fqdump.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/sra_fqdump.cfmod.pl -------------------------------------------------------------------------------- /modules/star.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/star.cfmod.pl -------------------------------------------------------------------------------- /modules/tophat.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/tophat.cfmod.pl -------------------------------------------------------------------------------- /modules/tophat_broken_MAPQ.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/tophat_broken_MAPQ.cfmod.pl -------------------------------------------------------------------------------- /modules/trim_galore.cfmod.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/modules/trim_galore.cfmod.pl -------------------------------------------------------------------------------- /pipelines/bam_preseq.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/pipelines/bam_preseq.config -------------------------------------------------------------------------------- /pipelines/bismark.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/pipelines/bismark.config -------------------------------------------------------------------------------- /pipelines/bismark_RRBS.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/pipelines/bismark_RRBS.config -------------------------------------------------------------------------------- /pipelines/bismark_pbat.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/pipelines/bismark_pbat.config -------------------------------------------------------------------------------- /pipelines/bismark_singlecell.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/pipelines/bismark_singlecell.config -------------------------------------------------------------------------------- /pipelines/bwa_preseq.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/pipelines/bwa_preseq.config -------------------------------------------------------------------------------- /pipelines/chipseq_qc.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/pipelines/chipseq_qc.config -------------------------------------------------------------------------------- /pipelines/fastq_bismark.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/pipelines/fastq_bismark.config -------------------------------------------------------------------------------- /pipelines/fastq_bismark_RRBS.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/pipelines/fastq_bismark_RRBS.config -------------------------------------------------------------------------------- /pipelines/fastq_bowtie.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/pipelines/fastq_bowtie.config -------------------------------------------------------------------------------- /pipelines/fastq_bowtie1_miRNA.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/pipelines/fastq_bowtie1_miRNA.config -------------------------------------------------------------------------------- /pipelines/fastq_hicup.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/pipelines/fastq_hicup.config -------------------------------------------------------------------------------- /pipelines/fastq_hisat2.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/pipelines/fastq_hisat2.config -------------------------------------------------------------------------------- /pipelines/fastq_pbat.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/pipelines/fastq_pbat.config -------------------------------------------------------------------------------- /pipelines/fastq_salmon.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/pipelines/fastq_salmon.config -------------------------------------------------------------------------------- /pipelines/fastq_star.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/pipelines/fastq_star.config -------------------------------------------------------------------------------- /pipelines/fastq_tophat.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/pipelines/fastq_tophat.config -------------------------------------------------------------------------------- /pipelines/sra_bismark.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/pipelines/sra_bismark.config -------------------------------------------------------------------------------- /pipelines/sra_bismark_RRBS.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/pipelines/sra_bismark_RRBS.config -------------------------------------------------------------------------------- /pipelines/sra_bowtie.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/pipelines/sra_bowtie.config -------------------------------------------------------------------------------- /pipelines/sra_bowtie1.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/pipelines/sra_bowtie1.config -------------------------------------------------------------------------------- /pipelines/sra_bowtie1_miRNA.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/pipelines/sra_bowtie1_miRNA.config -------------------------------------------------------------------------------- /pipelines/sra_bowtie2.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/pipelines/sra_bowtie2.config -------------------------------------------------------------------------------- /pipelines/sra_hicup.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/pipelines/sra_hicup.config -------------------------------------------------------------------------------- /pipelines/sra_hisat2.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/pipelines/sra_hisat2.config -------------------------------------------------------------------------------- /pipelines/sra_pbat.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/pipelines/sra_pbat.config -------------------------------------------------------------------------------- /pipelines/sra_tophat.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/pipelines/sra_tophat.config -------------------------------------------------------------------------------- /pipelines/sra_trim.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/pipelines/sra_trim.config -------------------------------------------------------------------------------- /pipelines/trim_bowtie_miRNA.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/pipelines/trim_bowtie_miRNA.config -------------------------------------------------------------------------------- /pipelines/trim_tophat.config: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/pipelines/trim_tophat.config -------------------------------------------------------------------------------- /source/CF/Constants.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/source/CF/Constants.pm -------------------------------------------------------------------------------- /source/CF/Headnodehelpers.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/source/CF/Headnodehelpers.pm -------------------------------------------------------------------------------- /source/CF/Helpers.pm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/source/CF/Helpers.pm -------------------------------------------------------------------------------- /source/CF/Helpers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/source/CF/Helpers.py -------------------------------------------------------------------------------- /source/CF/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/source/CF/__init__.py -------------------------------------------------------------------------------- /source/CF/cf_tests.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/source/CF/cf_tests.pl -------------------------------------------------------------------------------- /source/CF/html_email_template.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/source/CF/html_email_template.html -------------------------------------------------------------------------------- /source/CF/plaintext_email_template.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ewels/clusterflow/HEAD/source/CF/plaintext_email_template.txt --------------------------------------------------------------------------------