From 15122e72cfa633bc9b58af988e282511c1e3af11 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Wed, 20 Mar 2019 08:07:38 -0500
Subject: [PATCH] Make sum directories.
---
workflow/main.nf | 22 ++++++++++-----------
workflow/scripts/generate_versions.py | 28 +++++++++++++--------------
2 files changed, 25 insertions(+), 25 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index 1365f8c..7a1bed5 100644
--- a/workflow/main.nf
+++ b/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:
diff --git a/workflow/scripts/generate_versions.py b/workflow/scripts/generate_versions.py
index 786318f..b783f14 100644
--- a/workflow/scripts/generate_versions.py
+++ b/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+)"],
}
--
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