From 68c8f096b3f5204cce3948963b1ca221046a04b8 Mon Sep 17 00:00:00 2001 From: Adetunji Date: Tue, 28 Apr 2020 13:26:54 -0500 Subject: [PATCH] reorganized --- {scripts => bin}/BAM2GFF-local.sh | 0 {scripts => bin}/ROSE-local.sh | 0 {scripts => bin}/basicfastqstats.sh | 0 {scripts => bin}/chromatinSEreadjson.pl | 0 {scripts => bin}/flanking.pl | 0 {scripts => bin}/liquidator.pl | 0 {scripts => bin}/normalize_WIG_to_RPM.pl | 0 {scripts => bin}/readLength.sh | 0 {scripts => bin}/reorganize.sh | 0 {scripts => bin}/run_spp.R | 0 {scripts => bin}/summaryfacts.pl | 0 {scripts => bin}/tagLength.sh | 0 {tools => cwl}/ame.cwl | 0 {tools => cwl}/bamtobed.cwl | 0 tools/bamtogff-ALL.cwl => cwl/bamtogff.cwl | 0 {tools => cwl}/basicfastqstats.cwl | 0 {tools => cwl}/bedfasta.cwl | 0 {tools => cwl}/blacklist.cwl | 0 {tools => cwl}/bowtie.cwl | 0 {tools => cwl}/fastqc.cwl | 0 {tools => cwl}/flankbed.cwl | 0 {tools => cwl}/igvtdf.cwl | 0 {tools => cwl}/intersectbed.cwl | 0 {tools => cwl}/macs1call.cwl | 0 {tools => cwl}/macs1nm.cwl | 0 {tools => cwl}/meme-chip.cwl | 0 {subworkflows => cwl}/motifs.cwl | 6 +- {tools => cwl}/movealloutput.cwl | 0 {tools => cwl}/normalize.cwl | 0 tools/roseNC-ALL.cwl => cwl/roseNC.cwl | 0 {tools => cwl}/runSPP.cwl | 0 {tools => cwl}/samtools-flagstat.cwl | 0 {tools => cwl}/samtools-index.cwl | 0 {tools => cwl}/samtools-mkdupr.cwl | 0 {tools => cwl}/samtools-sort.cwl | 0 {tools => cwl}/samtools-view.cwl | 0 cwl/seaseq-mapping.cwl | 182 +++++++++++++++++++++ {workflows => cwl}/seaseq_pipeline.cwl | 66 ++++---- {tools => cwl}/sicer.cwl | 0 {tools => cwl}/sicerRB.cwl | 0 {tools => cwl}/sortbed.cwl | 0 {tools => cwl}/summarystats.cwl | 0 {tools => cwl}/taglength.cwl | 0 {subworkflows => cwl}/visualization.cwl | 6 +- {tools => cwl}/wigtobigwig.cwl | 0 inputparameters.yml | 30 ---- tools/bamtogff.cwl | 89 ---------- tools/roseNC.cwl | 68 -------- 48 files changed, 221 insertions(+), 226 deletions(-) rename {scripts => bin}/BAM2GFF-local.sh (100%) rename {scripts => bin}/ROSE-local.sh (100%) rename {scripts => bin}/basicfastqstats.sh (100%) rename {scripts => bin}/chromatinSEreadjson.pl (100%) rename {scripts => bin}/flanking.pl (100%) rename {scripts => bin}/liquidator.pl (100%) rename {scripts => bin}/normalize_WIG_to_RPM.pl (100%) rename {scripts => bin}/readLength.sh (100%) rename {scripts => bin}/reorganize.sh (100%) rename {scripts => bin}/run_spp.R (100%) rename {scripts => bin}/summaryfacts.pl (100%) rename {scripts => bin}/tagLength.sh (100%) rename {tools => cwl}/ame.cwl (100%) rename {tools => cwl}/bamtobed.cwl (100%) rename tools/bamtogff-ALL.cwl => cwl/bamtogff.cwl (100%) rename {tools => cwl}/basicfastqstats.cwl (100%) rename {tools => cwl}/bedfasta.cwl (100%) rename {tools => cwl}/blacklist.cwl (100%) rename {tools => cwl}/bowtie.cwl (100%) rename {tools => cwl}/fastqc.cwl (100%) rename {tools => cwl}/flankbed.cwl (100%) rename {tools => cwl}/igvtdf.cwl (100%) rename {tools => cwl}/intersectbed.cwl (100%) rename {tools => cwl}/macs1call.cwl (100%) rename {tools => cwl}/macs1nm.cwl (100%) rename {tools => cwl}/meme-chip.cwl (100%) rename {subworkflows => cwl}/motifs.cwl (93%) rename {tools => cwl}/movealloutput.cwl (100%) rename {tools => cwl}/normalize.cwl (100%) rename tools/roseNC-ALL.cwl => cwl/roseNC.cwl (100%) rename {tools => cwl}/runSPP.cwl (100%) rename {tools => cwl}/samtools-flagstat.cwl (100%) rename {tools => cwl}/samtools-index.cwl (100%) rename {tools => cwl}/samtools-mkdupr.cwl (100%) rename {tools => cwl}/samtools-sort.cwl (100%) rename {tools => cwl}/samtools-view.cwl (100%) create mode 100755 cwl/seaseq-mapping.cwl rename {workflows => cwl}/seaseq_pipeline.cwl (89%) rename {tools => cwl}/sicer.cwl (100%) rename {tools => cwl}/sicerRB.cwl (100%) rename {tools => cwl}/sortbed.cwl (100%) rename {tools => cwl}/summarystats.cwl (100%) rename {tools => cwl}/taglength.cwl (100%) rename {subworkflows => cwl}/visualization.cwl (90%) rename {tools => cwl}/wigtobigwig.cwl (100%) delete mode 100755 inputparameters.yml delete mode 100755 tools/bamtogff.cwl delete mode 100755 tools/roseNC.cwl diff --git a/scripts/BAM2GFF-local.sh b/bin/BAM2GFF-local.sh similarity index 100% rename from scripts/BAM2GFF-local.sh rename to bin/BAM2GFF-local.sh diff --git a/scripts/ROSE-local.sh b/bin/ROSE-local.sh similarity index 100% rename from scripts/ROSE-local.sh rename to bin/ROSE-local.sh diff --git a/scripts/basicfastqstats.sh b/bin/basicfastqstats.sh similarity index 100% rename from scripts/basicfastqstats.sh rename to bin/basicfastqstats.sh diff --git a/scripts/chromatinSEreadjson.pl b/bin/chromatinSEreadjson.pl similarity index 100% rename from scripts/chromatinSEreadjson.pl rename to bin/chromatinSEreadjson.pl diff --git a/scripts/flanking.pl b/bin/flanking.pl similarity index 100% rename from scripts/flanking.pl rename to bin/flanking.pl diff --git a/scripts/liquidator.pl b/bin/liquidator.pl similarity index 100% rename from scripts/liquidator.pl rename to bin/liquidator.pl diff --git a/scripts/normalize_WIG_to_RPM.pl b/bin/normalize_WIG_to_RPM.pl similarity index 100% rename from scripts/normalize_WIG_to_RPM.pl rename to bin/normalize_WIG_to_RPM.pl diff --git a/scripts/readLength.sh b/bin/readLength.sh similarity index 100% rename from scripts/readLength.sh rename to bin/readLength.sh diff --git a/scripts/reorganize.sh b/bin/reorganize.sh similarity index 100% rename from scripts/reorganize.sh rename to bin/reorganize.sh diff --git a/scripts/run_spp.R b/bin/run_spp.R similarity index 100% rename from scripts/run_spp.R rename to bin/run_spp.R diff --git a/scripts/summaryfacts.pl b/bin/summaryfacts.pl similarity index 100% rename from scripts/summaryfacts.pl rename to bin/summaryfacts.pl diff --git a/scripts/tagLength.sh b/bin/tagLength.sh similarity index 100% rename from scripts/tagLength.sh rename to bin/tagLength.sh diff --git a/tools/ame.cwl b/cwl/ame.cwl similarity index 100% rename from tools/ame.cwl rename to cwl/ame.cwl diff --git a/tools/bamtobed.cwl b/cwl/bamtobed.cwl similarity index 100% rename from tools/bamtobed.cwl rename to cwl/bamtobed.cwl diff --git a/tools/bamtogff-ALL.cwl b/cwl/bamtogff.cwl similarity index 100% rename from tools/bamtogff-ALL.cwl rename to cwl/bamtogff.cwl diff --git a/tools/basicfastqstats.cwl b/cwl/basicfastqstats.cwl similarity index 100% rename from tools/basicfastqstats.cwl rename to cwl/basicfastqstats.cwl diff --git a/tools/bedfasta.cwl b/cwl/bedfasta.cwl similarity index 100% rename from tools/bedfasta.cwl rename to cwl/bedfasta.cwl diff --git a/tools/blacklist.cwl b/cwl/blacklist.cwl similarity index 100% rename from tools/blacklist.cwl rename to cwl/blacklist.cwl diff --git a/tools/bowtie.cwl b/cwl/bowtie.cwl similarity index 100% rename from tools/bowtie.cwl rename to cwl/bowtie.cwl diff --git a/tools/fastqc.cwl b/cwl/fastqc.cwl similarity index 100% rename from tools/fastqc.cwl rename to cwl/fastqc.cwl diff --git a/tools/flankbed.cwl b/cwl/flankbed.cwl similarity index 100% rename from tools/flankbed.cwl rename to cwl/flankbed.cwl diff --git a/tools/igvtdf.cwl b/cwl/igvtdf.cwl similarity index 100% rename from tools/igvtdf.cwl rename to cwl/igvtdf.cwl diff --git a/tools/intersectbed.cwl b/cwl/intersectbed.cwl similarity index 100% rename from tools/intersectbed.cwl rename to cwl/intersectbed.cwl diff --git a/tools/macs1call.cwl b/cwl/macs1call.cwl similarity index 100% rename from tools/macs1call.cwl rename to cwl/macs1call.cwl diff --git a/tools/macs1nm.cwl b/cwl/macs1nm.cwl similarity index 100% rename from tools/macs1nm.cwl rename to cwl/macs1nm.cwl diff --git a/tools/meme-chip.cwl b/cwl/meme-chip.cwl similarity index 100% rename from tools/meme-chip.cwl rename to cwl/meme-chip.cwl diff --git a/subworkflows/motifs.cwl b/cwl/motifs.cwl similarity index 93% rename from subworkflows/motifs.cwl rename to cwl/motifs.cwl index 68e3ac6..92748bc 100755 --- a/subworkflows/motifs.cwl +++ b/cwl/motifs.cwl @@ -39,7 +39,7 @@ outputs: steps: MEMECHIP: - run: ../tools/meme-chip.cwl + run: meme-chip.cwl in: convertfasta: BEDfasta/outfile out: [outDir] @@ -49,7 +49,7 @@ steps: ResourceRequirement: ramMax: 10000 coresMin: 1 - run: ../tools/ame.cwl + run: ame.cwl in: convertfasta: BEDfasta/outfile motifdatabases: motifdatabases @@ -60,7 +60,7 @@ steps: reference: reference bedfile: bedfile out: [outfile] - run: ../tools/bedfasta.cwl + run: bedfasta.cwl doc: | diff --git a/tools/movealloutput.cwl b/cwl/movealloutput.cwl similarity index 100% rename from tools/movealloutput.cwl rename to cwl/movealloutput.cwl diff --git a/tools/normalize.cwl b/cwl/normalize.cwl similarity index 100% rename from tools/normalize.cwl rename to cwl/normalize.cwl diff --git a/tools/roseNC-ALL.cwl b/cwl/roseNC.cwl similarity index 100% rename from tools/roseNC-ALL.cwl rename to cwl/roseNC.cwl diff --git a/tools/runSPP.cwl b/cwl/runSPP.cwl similarity index 100% rename from tools/runSPP.cwl rename to cwl/runSPP.cwl diff --git a/tools/samtools-flagstat.cwl b/cwl/samtools-flagstat.cwl similarity index 100% rename from tools/samtools-flagstat.cwl rename to cwl/samtools-flagstat.cwl diff --git a/tools/samtools-index.cwl b/cwl/samtools-index.cwl similarity index 100% rename from tools/samtools-index.cwl rename to cwl/samtools-index.cwl diff --git a/tools/samtools-mkdupr.cwl b/cwl/samtools-mkdupr.cwl similarity index 100% rename from tools/samtools-mkdupr.cwl rename to cwl/samtools-mkdupr.cwl diff --git a/tools/samtools-sort.cwl b/cwl/samtools-sort.cwl similarity index 100% rename from tools/samtools-sort.cwl rename to cwl/samtools-sort.cwl diff --git a/tools/samtools-view.cwl b/cwl/samtools-view.cwl similarity index 100% rename from tools/samtools-view.cwl rename to cwl/samtools-view.cwl diff --git a/cwl/seaseq-mapping.cwl b/cwl/seaseq-mapping.cwl new file mode 100755 index 0000000..7d7c1ba --- /dev/null +++ b/cwl/seaseq-mapping.cwl @@ -0,0 +1,182 @@ +#!/usr/bin/env cwl-runner +cwlVersion: v1.0 +class: Workflow + +requirements: + - class: ScatterFeatureRequirement + - class: SubworkflowFeatureRequirement + +inputs: + reference: Directory + fastqfile: File[] + chromsizes: File + blacklistfile: File + best_alignments: boolean? + good_alignments: int? + limit_alignments: int? + processors: int? + +outputs: + sam_sort: + outputSource: SamSort/outfile + type: File[] + + fastq_metrics: + outputSource: BasicMetrics/metrics_out + type: File[] + + rmdup_bam: + outputSource: SamIndex/outfile + type: File[] + + bklist_bam: + outputSource: BkIndex/outfile + type: File[] + + bamqc_html: + outputSource: BamQC/htmlfile + type: File[] + + bamqc_zip: + outputSource: BamQC/zipfile + type: File[] + + readqc_zip: + outputSource: ReadQC/zipfile + type: File[] + + readqc_html: + outputSource: ReadQC/htmlfile + type: File[] + + stat_bk: + outputSource: STATbk/outfile + type: File[] + + stat_bam: + outputSource: STATbam/outfile + type: File[] + + stat_rmdup: + outputSource: STATrmdup/outfile + type: File[] + + +steps: + BasicMetrics: + requirements: + ResourceRequirement: + ramMax: 20000 + coresMin: 1 + in: + fastqfile: fastqfile + out: [metrics_out] + run: basicfastqstats.cwl + scatter: fastqfile + + TagLen: + in: + datafile: BasicMetrics/metrics_out + out: [tagLength] + run: taglength.cwl + scatter: datafile + + ReadQC: + in: + infile: fastqfile + out: [htmlfile, zipfile] + run: fastqc.cwl + scatter: infile + + Bowtie: + requirements: + ResourceRequirement: + ramMax: 10000 + coresMin: 20 + run: bowtie.cwl + in: + readLengthFile: TagLen/tagLength + best_alignments: best_alignments + good_alignments: good_alignments + fastqfile: fastqfile + limit_alignments: limit_alignments + processors: processors + reference: reference + out: [samfile] + scatter: [readLengthFile, fastqfile] + scatterMethod: dotproduct + + SamView: + in: + infile: Bowtie/samfile + out: [outfile] + run: samtools-view.cwl + scatter: infile + + BamQC: + in: + infile: SamView/outfile + out: [htmlfile, zipfile] + run: fastqc.cwl + scatter: infile + + SamSort: + in: + infile: SamView/outfile + out: [outfile] + run: samtools-sort.cwl + scatter: infile + + BkList: + in: + infile: SamSort/outfile + blacklistfile: blacklistfile + out: [outfile] + run: blacklist.cwl + scatter: infile + + BkIndex: + in: + infile: BkList/outfile + out: [outfile] + run: samtools-index.cwl + scatter: infile + + SamRMDup: + in: + infile: BkList/outfile + out: [outfile] + run: samtools-mkdupr.cwl + scatter: infile + + SamIndex: + in: + infile: SamRMDup/outfile + out: [outfile] + run: samtools-index.cwl + scatter: infile + + STATbam: + in: + infile: SamView/outfile + out: [outfile] + run: samtools-flagstat.cwl + scatter: infile + + STATrmdup: + in: + infile: SamRMDup/outfile + out: [outfile] + run: samtools-flagstat.cwl + scatter: infile + + STATbk: + in: + infile: BkList/outfile + out: [outfile] + run: samtools-flagstat.cwl + scatter: infile + + +doc: | + Runs ChIP-Seq SE Mapping FastQ SE files to generate BAM file for step 2 in ChIP-Seq Pipeline. diff --git a/workflows/seaseq_pipeline.cwl b/cwl/seaseq_pipeline.cwl similarity index 89% rename from workflows/seaseq_pipeline.cwl rename to cwl/seaseq_pipeline.cwl index 8960b7c..7bdb6d0 100755 --- a/workflows/seaseq_pipeline.cwl +++ b/cwl/seaseq_pipeline.cwl @@ -68,21 +68,21 @@ steps: in: fastqfile: fastqfile out: [metrics_out] - run: ../tools/basicfastqstats.cwl + run: basicfastqstats.cwl scatter: fastqfile TagLen: in: datafile: BasicMetrics/metrics_out out: [tagLength] - run: ../tools/taglength.cwl + run: taglength.cwl scatter: datafile ReadQC: in: infile: fastqfile out: [htmlfile, zipfile] - run: ../tools/fastqc.cwl + run: fastqc.cwl scatter: infile Bowtie: @@ -90,7 +90,7 @@ steps: ResourceRequirement: ramMax: 10000 coresMin: 20 - run: ../tools/bowtie.cwl + run: bowtie.cwl in: readLengthFile: TagLen/tagLength best_alignments: best_alignments @@ -107,21 +107,21 @@ steps: in: infile: Bowtie/samfile out: [outfile] - run: ../tools/samtools-view.cwl + run: samtools-view.cwl scatter: infile BamQC: in: infile: SamView/outfile out: [htmlfile, zipfile] - run: ../tools/fastqc.cwl + run: fastqc.cwl scatter: infile SamSort: in: infile: SamView/outfile out: [outfile] - run: ../tools/samtools-sort.cwl + run: samtools-sort.cwl scatter: infile BkList: @@ -129,49 +129,49 @@ steps: infile: SamSort/outfile blacklistfile: blacklistfile out: [outfile] - run: ../tools/blacklist.cwl + run: blacklist.cwl scatter: infile BkIndex: in: infile: BkList/outfile out: [outfile] - run: ../tools/samtools-index.cwl + run: samtools-index.cwl scatter: infile SamRMDup: in: infile: BkList/outfile out: [outfile] - run: ../tools/samtools-mkdupr.cwl + run: samtools-mkdupr.cwl scatter: infile SamIndex: in: infile: SamRMDup/outfile out: [outfile] - run: ../tools/samtools-index.cwl + run: samtools-index.cwl scatter: infile STATbam: in: infile: SamView/outfile out: [outfile] - run: ../tools/samtools-flagstat.cwl + run: samtools-flagstat.cwl scatter: infile STATrmdup: in: infile: SamRMDup/outfile out: [outfile] - run: ../tools/samtools-flagstat.cwl + run: samtools-flagstat.cwl scatter: infile STATbk: in: infile: BkList/outfile out: [outfile] - run: ../tools/samtools-flagstat.cwl + run: samtools-flagstat.cwl scatter: infile # PEAK CALLING & VISUALS @@ -187,7 +187,7 @@ steps: wiggle: wiggle single_profile: single_profile out: [ peaksbedfile, peaksxlsfile, summitsfile, wigfile, macsDir ] - run: ../tools/macs1call.cwl + run: macs1call.cwl scatter: treatmentfile WIG-Auto: @@ -196,7 +196,7 @@ steps: peaksxls: MACS-Auto/peaksxlsfile chromsizes: chromsizes out: [ rpmwig, outBW, outtdf ] - run: ../subworkflows/visualization.cwl + run: visualization.cwl scatter: [wigfile, peaksxls] scatterMethod: dotproduct @@ -213,7 +213,7 @@ steps: wiggle: wiggle single_profile: single_profile out: [ peaksbedfile, peaksxlsfile, summitsfile, wigfile, macsDir ] - run: ../tools/macs1call.cwl + run: macs1call.cwl scatter: treatmentfile WIG-All: @@ -222,7 +222,7 @@ steps: peaksxls: MACS-All/peaksxlsfile chromsizes: chromsizes out: [ rpmwig, outBW, outtdf ] - run: ../subworkflows/visualization.cwl + run: visualization.cwl scatter: [wigfile, peaksxls] scatterMethod: dotproduct @@ -237,7 +237,7 @@ steps: wiggle: wiggle single_profile: single_profile out: [ peaksbedfile, peaksxlsfile, summitsfile, wigfile, macsDir ] - run: ../tools/macs1nm.cwl + run: macs1nm.cwl scatter: treatmentfile WIG-NM: @@ -246,7 +246,7 @@ steps: peaksxls: MACS-NM/peaksxlsfile chromsizes: chromsizes out: [ rpmwig, outBW, outtdf ] - run: ../subworkflows/visualization.cwl + run: visualization.cwl scatter: [wigfile, peaksxls] scatterMethod: dotproduct @@ -257,7 +257,7 @@ steps: bedfile: MACS-Auto/peaksbedfile motifdatabases: motifdatabases out: [memechipdir, amedir, bedfasta] - run: ../subworkflows/motifs.cwl + run: motifs.cwl scatter: bedfile #SUMMIT-MOTIF analysis @@ -266,7 +266,7 @@ steps: bedfile: MACS-Auto/summitsfile flank: flank out: [outfile] - run: ../tools/flankbed.cwl + run: flankbed.cwl scatter: bedfile SummitMOTIFS: @@ -275,7 +275,7 @@ steps: bedfile: FlankBED/outfile motifdatabases: motifdatabases out: [memechipdir, amedir, bedfasta] - run: ../subworkflows/motifs.cwl + run: motifs.cwl scatter: bedfile # METAGENE analysis @@ -285,7 +285,7 @@ steps: gtffile: gtffile chromsizes: chromsizes out: [ metagenesDir ] - run: ../tools/bamtogff-ALL.cwl + run: bamtogff.cwl scatter: bamfile # SICER broad peaks caller @@ -293,7 +293,7 @@ steps: in: infile: SamIndex/outfile out: [ outfile ] - run: ../tools/bamtobed.cwl + run: bamtobed.cwl scatter: infile SICER: @@ -310,7 +310,7 @@ steps: gapsize: gapsize evalue: evalue treatmentbedfile: B2Bed/outfile - run: ../tools/sicer.cwl + run: sicer.cwl out: [ sicerDir ] scatter: treatmentbedfile @@ -328,7 +328,7 @@ steps: fileA: MACS-All/peaksbedfile fileB: MACS-Auto/peaksbedfile out: [ RoseDir ] - run: ../tools/roseNC-ALL.cwl + run: roseNC.cwl scatter: [bamfile, fileA, fileB] scatterMethod: dotproduct @@ -337,7 +337,7 @@ steps: in: infile: BkIndex/outfile out: [ outfile ] - run: ../tools/bamtobed.cwl + run: bamtobed.cwl scatter: infile SortBed: @@ -348,7 +348,7 @@ steps: in: infile: Bklist2Bed/outfile out: [outfile] - run: ../tools/sortbed.cwl + run: sortbed.cwl scatter: infile runSPP: @@ -359,7 +359,7 @@ steps: in: infile: BkIndex/outfile out: [spp_out] - run: ../tools/runSPP.cwl + run: runSPP.cwl scatter: infile CountIntersectBed: @@ -371,7 +371,7 @@ steps: peaksbed: MACS-Auto/peaksbedfile bamtobed: SortBed/outfile out: [outfile] - run: ../tools/intersectbed.cwl + run: intersectbed.cwl scatter: [peaksbed, bamtobed] scatterMethod: dotproduct @@ -392,7 +392,7 @@ steps: bkflag: STATbk/outfile rosedir: ROSE/RoseDir out: [ statsfile, htmlfile, textfile ] - run: ../tools/summarystats.cwl + run: summarystats.cwl scatter: [fastqmetrics, fastqczip, sppfile, bambed, countsfile, peaksxls, bamflag, rmdupflag, bkflag, rosedir] scatterMethod: dotproduct @@ -435,6 +435,6 @@ steps: htmlfile: PeaksQC/htmlfile textfile: PeaksQC/textfile out: [ finalDir ] - run: ../tools/movealloutput.cwl + run: movealloutput.cwl scatter: [ sam_sort, fastq_metrics, rmdup_bam, bklist_bam, bamqc_html, bamqc_zip, readqc_zip, readqc_html, macsDir, allmacsDir, nmmacsDir, rpmwig, outBW, outtdf, allrpmwig, alloutBW, allouttdf, nmrpmwig, nmoutBW, nmouttdf, bedfasta, flankbed, memechipdir, summitmemechipdir, amedir, summitamedir, metagenesDir, sicerDir, roseoutput, statsfile, htmlfile, textfile ] scatterMethod: dotproduct diff --git a/tools/sicer.cwl b/cwl/sicer.cwl similarity index 100% rename from tools/sicer.cwl rename to cwl/sicer.cwl diff --git a/tools/sicerRB.cwl b/cwl/sicerRB.cwl similarity index 100% rename from tools/sicerRB.cwl rename to cwl/sicerRB.cwl diff --git a/tools/sortbed.cwl b/cwl/sortbed.cwl similarity index 100% rename from tools/sortbed.cwl rename to cwl/sortbed.cwl diff --git a/tools/summarystats.cwl b/cwl/summarystats.cwl similarity index 100% rename from tools/summarystats.cwl rename to cwl/summarystats.cwl diff --git a/tools/taglength.cwl b/cwl/taglength.cwl similarity index 100% rename from tools/taglength.cwl rename to cwl/taglength.cwl diff --git a/subworkflows/visualization.cwl b/cwl/visualization.cwl similarity index 90% rename from subworkflows/visualization.cwl rename to cwl/visualization.cwl index 9947262..8f92a16 100755 --- a/subworkflows/visualization.cwl +++ b/cwl/visualization.cwl @@ -45,18 +45,18 @@ steps: wigfile: wigfile peaksxls: peaksxls out: [RPMwig] - run: ../tools/normalize.cwl + run: normalize.cwl WIG: in: infile: RPM/RPMwig chromsizes: chromsizes out: [outfile] - run: ../tools/wigtobigwig.cwl + run: wigtobigwig.cwl TDF: in: wigfile: wigfile out: [outfile] - run: ../tools/igvtdf.cwl + run: igvtdf.cwl diff --git a/tools/wigtobigwig.cwl b/cwl/wigtobigwig.cwl similarity index 100% rename from tools/wigtobigwig.cwl rename to cwl/wigtobigwig.cwl diff --git a/inputparameters.yml b/inputparameters.yml deleted file mode 100755 index 86212f1..0000000 --- a/inputparameters.yml +++ /dev/null @@ -1,30 +0,0 @@ -#Files and Directories - -reference: - class: Directory - location: /rgs01/project_space/abrahgrp/Software_Dev_Sandbox/common/madetunj/genomes/hg19/TOPHAT - -fastqfile: - - { class: File, path: /rgs01/project_space/abrahgrp/Software_Dev_Sandbox/common/madetunj/fastqfiles/20190611_pL-EV_H3K27me3_MWZ7030_S1_R1_001.fastq.gz } - - { class: File, path: /rgs01/project_space/abrahgrp/Software_Dev_Sandbox/common/madetunj/fastqfiles/20190611_pL-P44L_H3K27ac_MWZ7030_S10_R1_001.fastq.gz } - - { class: File, path: /rgs01/project_space/abrahgrp/Software_Dev_Sandbox/common/madetunj/fastqfiles/20190628_KOPTK1-DMSO-MYBL2_AD7124_S12_R1_001.fastq.gz } - -keep_dup: all - -chromsizes: - class: File - path: /rgs01/project_space/abrahgrp/Software_Dev_Sandbox/common/madetunj/genomes/hg19/UCSC_CHROMSIZES/UCSC_hg19_chromInfo.tab - -blacklistfile: - class: File - path: /rgs01/project_space/abrahgrp/Software_Dev_Sandbox/common/madetunj/genomes/hg19/hg19-blacklist.v2.bed - -gtffile: - class: File - path: /rgs01/project_space/abrahgrp/Software_Dev_Sandbox/common/madetunj/genomes/hg19/GTF/GRCh37_latest_changed_genomic.gtf - -motifdatabases: - - { class: File, path: /rgs01/project_space/abrahgrp/Software_Dev_Sandbox/common/madetunj/motif_databases/JASPAR/JASPAR2018_CORE_vertebrates_redundant.meme } - - { class: File, path: /rgs01/project_space/abrahgrp/Software_Dev_Sandbox/common/madetunj/motif_databases/EUKARYOTE/jolma2013.meme } - - { class: File, path: /rgs01/project_space/abrahgrp/Software_Dev_Sandbox/common/madetunj/motif_databases/CIS-BP/Homo_sapiens.meme } - - { class: File, path: /rgs01/project_space/abrahgrp/Software_Dev_Sandbox/common/madetunj/motif_databases/HUMAN/HOCOMOCOv11_full_HUMAN_mono_meme_format.meme } diff --git a/tools/bamtogff.cwl b/tools/bamtogff.cwl deleted file mode 100755 index b0a4a66..0000000 --- a/tools/bamtogff.cwl +++ /dev/null @@ -1,89 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.0 -baseCommand: [BAM2GFF-local.sh] -class: CommandLineTool -label: BAM to GFF for MetaGenes calculation v1 on bam file for all metagenes -doc: | - BAM2GFF_call.sh - -requirements: -- class: ShellCommandRequirement -- class: InlineJavascriptRequirement - expressionLib: - - var var_output_name = function() { - if (inputs.samplename == ""){ - return inputs.bamfile.nameroot; - } - }; - -inputs: - bamfile: - label: "BAM file" - type: File - inputBinding: - position: 3 - secondaryFiles: - - .bai - - gtffile: - type: File - label: "GTF file" - inputBinding: - position: 1 - - chromsizes: - type: File - label: "Chromosome sizes tab file" - inputBinding: - position: 4 - - feature: - type: string? - label: "Feature Type" - default: "gene" - inputBinding: - position: 2 - - samplename: - type: string? - label: "Output file prefix" - inputBinding: - position: 5 - valueFrom: | - ${ - if (self == ""){ - return var_output_name(); - } else { - return self; - } - } - default: "" - - outputfolder: - type: string? - label: "Output directory name" - inputBinding: - position: 999 - shellQuote: false - separate: false - prefix: ' && nameoffolder="' - default: "bamdensity_out" - - verifymove: - type: boolean? - label: "Move files to new directory" - inputBinding: - position: 1000 - shellQuote: false - prefix: '" && mkdir -p $nameoffolder && mv matrix *png *pdf $nameoffolder' - default: true - -outputs: - metagenesDir: - type: Directory - label: "Output directory" - outputBinding: - glob: | - ${ - return inputs.outputfolder; - } diff --git a/tools/roseNC.cwl b/tools/roseNC.cwl deleted file mode 100755 index 3bb5ee2..0000000 --- a/tools/roseNC.cwl +++ /dev/null @@ -1,68 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.0 -baseCommand: [ROSE-local.sh] -class: CommandLineTool -label: ROSE - calling Enhancers and Super-enhancers -doc: | - ROSE_call.sh ROSE_out genes hg19 - -requirements: -- class: InlineJavascriptRequirement - -inputs: - gtffile: - type: File - label: "GTF file" - inputBinding: - position: 1 - - bamfile: - type: File - label: "BAM file" - inputBinding: - position: 2 - secondaryFiles: - - .bai - - outputdir: - type: string - label: "Output directory name" - default: "ROSE_out" - inputBinding: - position: 3 - - feature: - type: string? - label: "Feature Type" - default: "gene" - inputBinding: - position: 4 - - species: - type: string? - label: "Genome name" - default: "hg19" - inputBinding: - position: 5 - - fileA: - type: File - label: "MACS Auto BED file" - inputBinding: - position: 6 - - fileB: - type: File - label: "MACS All BED file" - inputBinding: - position: 7 - -outputs: - RoseDir: - type: Directory - label: "ROSE output directory" - outputBinding: - glob: | - ${ - return inputs.outputdir; - }