From b88cbb2e3f355bc4c62c258fd7c77bd408783496 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Wed, 13 Mar 2019 11:00:03 -0500
Subject: [PATCH] Update versions.
---
docs/references.md | 2 +-
workflow/main.nf | 36 ++++++++++++++++++---------
workflow/scripts/generate_versions.py | 6 -----
3 files changed, 25 insertions(+), 19 deletions(-)
diff --git a/docs/references.md b/docs/references.md
index b8f12b7..6998a59 100644
--- a/docs/references.md
+++ b/docs/references.md
@@ -4,7 +4,7 @@
* Anaconda (Anaconda Software Distribution, [https://anaconda.com](https://anaconda.com))
2. **trimgalore**:
- * trimgalore/0.4.1 [https://github.com/FelixKrueger/TrimGalore](https://github.com/FelixKrueger/TrimGalore)
+ * trimgalore [https://github.com/FelixKrueger/TrimGalore](https://github.com/FelixKrueger/TrimGalore)
3. **cutadapt**:
* Marcel, M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17(1):10-12. doi:[10.14806/ej.17.1.200](http://dx.doi.org/10.14806/ej.17.1.200)
diff --git a/workflow/main.nf b/workflow/main.nf
index 93334c7..f89abdb 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -489,17 +489,17 @@ process softwareReport {
input:
- trimReadsVersions.collect()
- alignReadsVersions.collect()
- filterReadsVersions.collect()
- convertReadsVersions.collect()
- crossReadsVersions.collect()
- callPeaksMACSVersions.collect()
- consensusPeaksVersions.collect()
- peakAnnotationVersions.collect()
- motifSearchVersions.collect()
- diffPeaksVersions.collect()
- experimentQCVersions.collect()
+ file trimReads_vf from trimReadsVersions.collect()
+ file alignReads_vf from alignReadsVersions.collect()
+ file filterReads_vf from filterReadsVersions.collect()
+ file convertReads_vf from convertReadsVersions.collect()
+ file crossReads_vf from crossReadsVersions.collect()
+ file callPeaksMACS_vf from callPeaksMACSVersions.collect()
+ file consensusPeaks_vf from consensusPeaksVersions.collect()
+ file peakAnnotation_vf from peakAnnotationVersions.collect()
+ file motifSearch_vf from motifSearchVersions.collect()
+ file diffPeaks_vf from diffPeaksVersions.collect()
+ file experimentQC_vf from experimentQCVersions.collect()
output:
@@ -509,7 +509,19 @@ process softwareReport {
script:
"""
echo $workflow.nextflow.version > version_nextflow.txt
- python3 $baseDir/scripts/generate_versions.py -f *.txt -o software_versions
python3 $baseDir/scripts/generate_references.py -r $references -o software_references
+ python3 $baseDir/scripts/generate_versions.py -f $trimReads_vf \
+ $alignReads_vf \
+ $filterReads_vf \
+ $convertReads_vf \
+ $crossReads_vf \
+ $callPeaksMACS_vf \
+ $consensusPeaks_vf \
+ $motifSearch_vf \
+ $diffPeaks_vf \
+ $experimentQC_vf \
+ version_nextflow.txt \
+ -o software_versions
+
"""
}
diff --git a/workflow/scripts/generate_versions.py b/workflow/scripts/generate_versions.py
index d4dd7fb..786318f 100644
--- a/workflow/scripts/generate_versions.py
+++ b/workflow/scripts/generate_versions.py
@@ -68,12 +68,6 @@ def check_files(files):
software_files = np.array(list(SOFTWARE_REGEX.values()))[:,0]
- missing_files = set(software_files) - set(files)
-
- if len(missing_files) > 0:
- logger.error('Missing version files: %s', list(missing_files))
- raise Exception("Missing version files: %s" % list(missing_files))
-
extra_files = set(files) - set(software_files)
if len(extra_files) > 0:
--
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