Update versions.

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)

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
+
   """
 }

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: