reorganized

madetunj · Apr 28, 2020 · 68c8f09 · 68c8f09
1 parent 51241c9
commit 68c8f09
Show file tree

Hide file tree

Showing 48 changed files with 221 additions and 226 deletions.
diff --git a/scripts/BAM2GFF-local.sh → bin/BAM2GFF-local.sh b/scripts/BAM2GFF-local.sh → bin/BAM2GFF-local.sh
diff --git a/scripts/ROSE-local.sh → bin/ROSE-local.sh b/scripts/ROSE-local.sh → bin/ROSE-local.sh
diff --git a/scripts/basicfastqstats.sh → bin/basicfastqstats.sh b/scripts/basicfastqstats.sh → bin/basicfastqstats.sh
diff --git a/scripts/chromatinSEreadjson.pl → bin/chromatinSEreadjson.pl b/scripts/chromatinSEreadjson.pl → bin/chromatinSEreadjson.pl
diff --git a/scripts/flanking.pl → bin/flanking.pl b/scripts/flanking.pl → bin/flanking.pl
diff --git a/scripts/liquidator.pl → bin/liquidator.pl b/scripts/liquidator.pl → bin/liquidator.pl
diff --git a/scripts/normalize_WIG_to_RPM.pl → bin/normalize_WIG_to_RPM.pl b/scripts/normalize_WIG_to_RPM.pl → bin/normalize_WIG_to_RPM.pl
diff --git a/scripts/readLength.sh → bin/readLength.sh b/scripts/readLength.sh → bin/readLength.sh
diff --git a/scripts/reorganize.sh → bin/reorganize.sh b/scripts/reorganize.sh → bin/reorganize.sh
diff --git a/scripts/run_spp.R → bin/run_spp.R b/scripts/run_spp.R → bin/run_spp.R
diff --git a/scripts/summaryfacts.pl → bin/summaryfacts.pl b/scripts/summaryfacts.pl → bin/summaryfacts.pl
diff --git a/scripts/tagLength.sh → bin/tagLength.sh b/scripts/tagLength.sh → bin/tagLength.sh
diff --git a/tools/ame.cwl → cwl/ame.cwl b/tools/ame.cwl → cwl/ame.cwl
diff --git a/tools/bamtobed.cwl → cwl/bamtobed.cwl b/tools/bamtobed.cwl → cwl/bamtobed.cwl
diff --git a/tools/bamtogff-ALL.cwl → cwl/bamtogff.cwl b/tools/bamtogff-ALL.cwl → cwl/bamtogff.cwl
diff --git a/tools/basicfastqstats.cwl → cwl/basicfastqstats.cwl b/tools/basicfastqstats.cwl → cwl/basicfastqstats.cwl
diff --git a/tools/bedfasta.cwl → cwl/bedfasta.cwl b/tools/bedfasta.cwl → cwl/bedfasta.cwl
diff --git a/tools/blacklist.cwl → cwl/blacklist.cwl b/tools/blacklist.cwl → cwl/blacklist.cwl
diff --git a/tools/bowtie.cwl → cwl/bowtie.cwl b/tools/bowtie.cwl → cwl/bowtie.cwl
diff --git a/tools/fastqc.cwl → cwl/fastqc.cwl b/tools/fastqc.cwl → cwl/fastqc.cwl
diff --git a/tools/flankbed.cwl → cwl/flankbed.cwl b/tools/flankbed.cwl → cwl/flankbed.cwl
diff --git a/tools/igvtdf.cwl → cwl/igvtdf.cwl b/tools/igvtdf.cwl → cwl/igvtdf.cwl
diff --git a/tools/intersectbed.cwl → cwl/intersectbed.cwl b/tools/intersectbed.cwl → cwl/intersectbed.cwl
diff --git a/tools/macs1call.cwl → cwl/macs1call.cwl b/tools/macs1call.cwl → cwl/macs1call.cwl
diff --git a/tools/macs1nm.cwl → cwl/macs1nm.cwl b/tools/macs1nm.cwl → cwl/macs1nm.cwl
diff --git a/tools/meme-chip.cwl → cwl/meme-chip.cwl b/tools/meme-chip.cwl → cwl/meme-chip.cwl
diff --git a/subworkflows/motifs.cwl → cwl/motifs.cwl b/subworkflows/motifs.cwl → 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 → cwl/movealloutput.cwl b/tools/movealloutput.cwl → cwl/movealloutput.cwl
diff --git a/tools/normalize.cwl → cwl/normalize.cwl b/tools/normalize.cwl → cwl/normalize.cwl
diff --git a/tools/roseNC-ALL.cwl → cwl/roseNC.cwl b/tools/roseNC-ALL.cwl → cwl/roseNC.cwl
diff --git a/tools/runSPP.cwl → cwl/runSPP.cwl b/tools/runSPP.cwl → cwl/runSPP.cwl
diff --git a/tools/samtools-flagstat.cwl → cwl/samtools-flagstat.cwl b/tools/samtools-flagstat.cwl → cwl/samtools-flagstat.cwl
diff --git a/tools/samtools-index.cwl → cwl/samtools-index.cwl b/tools/samtools-index.cwl → cwl/samtools-index.cwl
diff --git a/tools/samtools-mkdupr.cwl → cwl/samtools-mkdupr.cwl b/tools/samtools-mkdupr.cwl → cwl/samtools-mkdupr.cwl
diff --git a/tools/samtools-sort.cwl → cwl/samtools-sort.cwl b/tools/samtools-sort.cwl → cwl/samtools-sort.cwl
diff --git a/tools/samtools-view.cwl → cwl/samtools-view.cwl b/tools/samtools-view.cwl → cwl/samtools-view.cwl
diff --git a/cwl/seaseq-mapping.cwl 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.