Add seqtype override

CHANGELOG.md

 # 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)

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

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)