Make sum directories.

workflow/main.nf

@@ -491,17 +491,17 @@ process softwareReport {
 
   input:
 
-  file trimReads_vf from trimReadsVersions.first()
-  file alignReads_vf from alignReadsVersions.first()
-  file filterReads_vf from filterReadsVersions.first()
-  file convertReads_vf from convertReadsVersions.first()
-  file crossReads_vf from crossReadsVersions.first()
-  file callPeaksMACS_vf from callPeaksMACSVersions.first()
-  file consensusPeaks_vf from consensusPeaksVersions.first()
-  file peakAnnotation_vf from peakAnnotationVersions.first()
-  file motifSearch_vf from motifSearchVersions.first().ifEmpty()
-  file diffPeaks_vf from diffPeaksVersions.first().ifEmpty()
-  file experimentQC_vf from experimentQCVersions.first()
+  file 'trimReads_vf/*txt' from trimReadsVersions.first()
+  file 'alignReads_vf/*' from alignReadsVersions.first()
+  file 'filterReads_vf/*' from filterReadsVersions.first()
+  file 'convertReads_vf/*' from convertReadsVersions.first()
+  file 'crossReads_vf/*' from crossReadsVersions.first()
+  file 'callPeaksMACS_vf/*' from callPeaksMACSVersions.first()
+  file 'consensusPeaks_vf/*' from consensusPeaksVersions.first()
+  file 'peakAnnotation_vf/*' from peakAnnotationVersions.first()
+  file 'motifSearch_vf/*' from motifSearchVersions.first().ifEmpty()
+  file 'diffPeaks_vf/*' from diffPeaksVersions.first().ifEmpty()
+  file 'experimentQC_vf/*' from experimentQCVersions.first()
 
   output:
 

workflow/scripts/generate_versions.py

@@ -24,20 +24,20 @@ logger.setLevel(logging.INFO)
 
 SOFTWARE_REGEX = {
     'Nextflow': ['version_nextflow.txt', r"(\S+)"],
-    'Trim Galore!': ['version_trimgalore.txt', r"version (\S+)"],
-    'Cutadapt': ['version_cutadapt.txt', r"Version (\S+)"],
-    'BWA': ['version_bwa.txt', r"Version: (\S+)"],
-    'Samtools': ['version_samtools.txt', r"samtools (\S+)"],
-    'Sambamba': ['version_sambamba.txt', r"sambamba (\S+)"],
-    'BEDTools': ['version_bedtools.txt', r"bedtools v(\S+)"],
-    'R': ['version_r.txt', r"R version (\S+)"],
-    'SPP': ['version_spp.txt', r"\[1\] ‘(1.14)’"],
-    'MACS2': ['version_macs.txt', r"macs2 (\S+)"],
-    'bedGraphToBigWig': ['version_bedGraphToBigWig.txt', r"bedGraphToBigWig v (\S+)"],
-    'ChIPseeker': ['version_ChIPseeker.txt', r"Version (\S+)\""],
-    'MEME-ChIP': ['version_memechip.txt', r"Version (\S+)"],
-    'DiffBind': ['version_DiffBind.txt', r"Version (\S+)\""],
-    'deepTools': ['version_deeptools.txt', r"deeptools (\S+)"],
+    'Trim Galore!': ['trimReads_vf/version_trimgalore.txt', r"version (\S+)"],
+    'Cutadapt': ['trimReads_vf/version_cutadapt.txt', r"Version (\S+)"],
+    'BWA': ['alignReads_vf/version_bwa.txt', r"Version: (\S+)"],
+    'Samtools': ['filterReads_vf/alignReads_vf/version_samtools.txt', r"samtools (\S+)"],
+    'Sambamba': ['filterReads_vf/version_sambamba.txt', r"sambamba (\S+)"],
+    'BEDTools': ['convertReads_vf/version_bedtools.txt', r"bedtools v(\S+)"],
+    'R': ['crossReads_vf/version_r.txt', r"R version (\S+)"],
+    'SPP': ['crossReads_vf/version_spp.txt', r"\[1\] ‘(1.14)’"],
+    'MACS2': ['callPeaksMACS_vf/version_macs.txt', r"macs2 (\S+)"],
+    'bedGraphToBigWig': ['callPeaksMACS_vf/version_bedGraphToBigWig.txt', r"bedGraphToBigWig v (\S+)"],
+    'ChIPseeker': ['peakAnnotation_vf/version_ChIPseeker.txt', r"Version (\S+)\""],
+    'MEME-ChIP': ['motifSearch_vf/version_memechip.txt', r"Version (\S+)"],
+    'DiffBind': ['diffPeaks_vf/version_DiffBind.txt', r"Version (\S+)\""],
+    'deepTools': ['experimentQC_vf/version_deeptools.txt', r"deeptools (\S+)"],
 }