From f606ed669a998df32894fbcc2576249a3c2cade3 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 23 Jul 2021 11:40:24 -0500
Subject: [PATCH] Add seqtype override
---
CHANGELOG.md | 1 +
README.md | 2 ++
rna-seq.nf | 16 +++++++++++++++-
3 files changed, 18 insertions(+), 1 deletion(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4a27c94..c24a82f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,7 @@
# v.2.0.1 (indev)
**User Facing**
* Corrected spelling of inferred (#125)
+* Add seqtype force parameter (#131)
**Background**
* Corrected file search parameters due to name inconsistency (#129)
diff --git a/README.md b/README.md
index 1c505f9..80c4c65 100644
--- a/README.md
+++ b/README.md
@@ -63,6 +63,8 @@ To Run:
* eg: `--inputBagForce test_data/bag/Q-Y5F6_inputBag_xxxxxxxx.zip` (must be the expected bag structure, this example will not work because it is a test bag)
* `--fastqsForce` utilizes local fastq's instead of downloading from the data-hub (still requires accurate repRID input)
* eg: `--fastqsForce 'test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz'` (note the quotes around fastq's which must me named in the correct standard [*\*.R1.fastq.gz and/or \*.R2.fastq.gz*] and in the correct order, also consider using `endsForce` if the endness doesn't match submitted value)
+ * `--seqtypeForce` forces the sequencing type to be mRNAseq, it bypasses a inferred mismatch or an ambiguous error
+ * eg: `--seqtypeForce 'mRNAseq'`
* `--speciesForce` forces the species to be "Mus musculus" or "Homo sapiens", it bypasses a metadata mismatch or an ambiguous species error
* eg: `--speciesForce 'Mus musculus'`
* `--endsForce` forces the endness to be "se", or "pe", it bypasses a metadata mismatch error
diff --git a/rna-seq.nf b/rna-seq.nf
index 604fdaf..bbe62c7 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -36,6 +36,7 @@ params.endsForce = ""
params.speciesForce = ""
params.strandedForce = ""
params.spikeForce = ""
+params.seqtypeForce = ""
// Define tracking input variables
params.ci = false
@@ -76,6 +77,7 @@ endsForce = params.endsForce
speciesForce = params.speciesForce
strandedForce = params.strandedForce
spikeForce = params.spikeForce
+seqtypeForce = params.seqtypeForce
email = params.email
// Define fixed files and variables
@@ -926,6 +928,14 @@ process seqwho {
fi
fi
+ # override seqtype if forced
+ if [ "${params.seqtypeForce}" == "mRNAseq" ]
+ then
+ seqtypeError=false
+ seqtypeError_details=""
+ echo -e "LOG: seqtype Inferred R1=\${seqtypeR1}; Inferred R2=\${seqtypeR2}; Forced=mRNAseq" >> ${repRID}.seqwho.log
+ fi
+
# check for species match error
if [ "${speciesMeta}" != "\${speciesInfer}" ]
then
@@ -2117,7 +2127,7 @@ process aggrQC {
ulimit -a >> ${repRID}.aggrQC.log
# make run table
- if [ "${params.inputBagForce}" == "" ] && [ "${params.fastqsForce}" == "" ] && [ "${params.speciesForce}" == "" ] && [ "${params.strandedForce}" == "" ] && [ "${params.spikeForce}" == "" ]
+ if [ "${params.inputBagForce}" == "" ] && [ "${params.fastqsForce}" == "" ] && [ "${params.seqtypeForce}" == "" ] && [ "${params.speciesForce}" == "" ] && [ "${params.strandedForce}" == "" ] && [ "${params.spikeForce}" == "" ]
then
input="default"
else
@@ -2130,6 +2140,10 @@ process aggrQC {
then
input=\$(echo \${input} fastq)
fi
+ if [ "${params.seqtypeForce}" == "mRNAseq" ]
+ then
+ input=\$(echo \${input} seqtype)
+ fi
if [ "${params.speciesForce}" != "" ]
then
input=\$(echo \${input} species)
--
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