Collect the read counts from the input files

sanger-tol · Nov 6, 2023 · bdd1c2e · bdd1c2e
1 parent 093b313
commit bdd1c2e
Showing 1 changed file with 29 additions and 11 deletions.
diff --git a/subworkflows/local/input_check.nf b/subworkflows/local/input_check.nf
@@ -3,6 +3,7 @@
 //
 
 include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check'
+include { SAMTOOLS_FLAGSTAT } from '../../modules/nf-core/samtools/flagstat/main'
 
 
 workflow INPUT_CHECK {
@@ -11,20 +12,35 @@ workflow INPUT_CHECK {
 
 
     main:
+    ch_versions = Channel.empty()
+
+    // Read the samplesheet
     SAMPLESHEET_CHECK ( samplesheet ).csv
     | splitCsv ( header:true, sep:',' )
-    | map { create_data_channel( it ) }
+    // Prepare the channel for SAMTOOLS_FLAGSTAT
+    | map { row -> [row + [id: file(row.datafile).baseName], file(row.datafile, checkIfExists: true), []] }
+    | set { samplesheet_rows }
+    ch_versions = ch_versions.mix ( SAMPLESHEET_CHECK.out.versions.first() )
+
+    // Get stats from each input file
+    SAMTOOLS_FLAGSTAT ( samplesheet_rows )
+    ch_versions = ch_versions.mix ( SAMTOOLS_FLAGSTAT.out.versions.first() )
+
+    // Create the read channel for the rest of the pipeline
+    samplesheet_rows
+    | join( SAMTOOLS_FLAGSTAT.out.flagstat )
+    | map { meta, datafile, dummy, stats -> create_data_channel( meta, datafile, stats ) }
     | set { reads }
 
 
     emit:
     reads                                        // channel: [ val(meta), /path/to/datafile ]
-    versions = SAMPLESHEET_CHECK.out.versions    // channel: [ versions.yml ]
+    versions = ch_versions                       // channel: [ versions.yml ]
 }
 
 
 // Function to get list of [ meta, reads ]
-def create_data_channel ( LinkedHashMap row ) {
+def create_data_channel ( LinkedHashMap row, datafile, stats ) {
     // create meta map
     def meta = [:]
     meta.id         = row.sample
@@ -39,13 +55,15 @@ def create_data_channel ( LinkedHashMap row ) {
     }
     meta.read_group  = "\'@RG\\tID:" + row.datafile.split('/')[-1].split('\\.')[0] + "\\tPL:" + platform + "\\tSM:" + meta.id.split('_')[0..-2].join('_') + "\'"
 
-
-    // add path(s) of the read file(s) to the meta map
-    def data_meta = []
-    if ( !file(row.datafile).exists() ) {
-        exit 1, "ERROR: Please check input samplesheet -> Data file does not exist!\n${row.datafile}"
-    } else {
-        data_meta = [ meta, file(row.datafile) ]
+    // Read the first line of the flagstat file
+    // 3127898040 + 0 in total (QC-passed reads + QC-failed reads)
+    // and make the sum of both integers
+    stats.withReader {
+        line = it.readLine()
+        def lspl = line.split()
+        def read_count = lspl[0].toInteger() + lspl[2].toInteger()
+        meta.read_count = read_count
     }
-    return data_meta
+
+    return [meta, datafile]
 }