diff --git a/CHANGELOG.md b/CHANGELOG.md index f7c6e7434ded3fae226e7f37dc60d4c88f15cd39..deaa3b985febeaffe0660b2d296c83a69bb1a4a8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,8 @@ **Background** * Add memory limit per thread for samtools sort +* Remove parsing restrictions for submitted stranded/spike/species +* Pass unidentified ends instead of overwriting it as unknown *Known Bugs* * Override params (inputBag, fastq, species) aren't checked for integrity diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index abec0190f6901d66f0f84be07a3f4eff51b8992e..fcf77a38b387188caff1ae661fb4bdcbc36540ee 100644 --- a/workflow/rna-seq.nf +++ b/workflow/rna-seq.nf @@ -338,7 +338,7 @@ process parseMetadata { then endsMeta="pe" else - endsMeta="unknown" + endsMeta=\${endsRaw} fi if [ "\${endsRaw}" == "" ] then diff --git a/workflow/scripts/parse_meta.py b/workflow/scripts/parse_meta.py index 12cc7c7233b94509e5c3a7307e8ef7985a94a958..c2c71e008d6d43f45c4e0637d01240d2b6b07a67 100644 --- a/workflow/scripts/parse_meta.py +++ b/workflow/scripts/parse_meta.py @@ -43,7 +43,7 @@ def main(): # Check experiment RID metadata from 'Experiment.csv' if (args.parameter == "expRID"): if (len(metaFile.Experiment_RID.unique()) > 1): - print("There are multiple experoment RID's in the metadata: " + + print("There are multiple experiment RID's in the metadata: " + " ".join(metaFile.Experiment_RID.unique())) exit(1) else: @@ -79,10 +79,6 @@ def main(): stranded = "stranded" elif (metaFile.Has_Strand_Specific_Information.unique() == "no"): stranded = "unstranded" - else: - print("Stranded metadata not match expected options: " + - metaFile.Has_Strand_Specific_Information.unique()) - exit(1) print(stranded) # Get spike-in metadata from 'Experiment Settings.csv' @@ -91,10 +87,6 @@ def main(): spike = "yes" elif (metaFile.Used_Spike_Ins.unique() == "no"): spike = "no" - else: - print("Spike-ins metadata not match expected options: " + - metaFile.Used_Spike_Ins.unique()) - exit(1) print(spike) # Get species metadata from 'Experiment.csv' @@ -103,10 +95,6 @@ def main(): species = "Mus musculus" elif (metaFile.Species.unique() == "Homo sapiens"): species = "Homo sapiens" - else: - print("Species metadata not match expected options: " + - metaFile.Species.unique()) - exit(1) print(species) # Get read length metadata from 'Experiment Settings.csv'