2nd Parity update to 1.1.1 treeval

bin/generate_cram_csv.sh

@@ -1,29 +1,82 @@
 #!/bin/bash
-cram_path=$1
-chunkn=0
-for cram in ${cram_path}/*.cram; do
-    rgline=$(samtools view -H $cram|grep "RG"|sed 's/\t/\\t/g'|sed "s/'//g")
 
-    crampath=$(readlink -f ${cram})
+# generate_cram_csv.sh
+# -------------------
+# Generate a csv file describing the CRAM folder
+# ><((((°>    Y    ><((((°>    U     ><((((°>    M     ><((((°>     I     ><((((°>
+# Author = yy5
+# ><((((°>    Y    ><((((°>    U     ><((((°>    M     ><((((°>     I     ><((((°>
 
-    ncontainers=$(zcat ${crampath}.crai|wc -l)
-    base=$(basename $cram .cram)
+# Function to process chunking of a CRAM file
+chunk_cram() {
+    local cram=$1
+    local chunkn=$2
+    local outcsv=$3
+    realcram=$(readlink -f ${cram})
+    realcrai=$(readlink -f ${cram}.crai)
+    local rgline=$(samtools view -H "${realcram}" | grep "@RG" | sed 's/\t/\\t/g' | sed "s/'//g")
+    local ncontainers=$(zcat "${realcrai}" | wc -l)
+    local base=$(basename "${realcram}" .cram)
+    local from=0
+    local to=10000
 
-    from=0
-    to=10000
 
-
-    while [ $to -lt $ncontainers ]
-    do
-        echo $crampath,${crampath}.crai,${from},${to},${base},${chunkn},${rgline}
-        from=$((to+1))
-        ((to+=10000))
+    while [ $to -lt $ncontainers ]; do
+        echo "${realcram},${realcrai},${from},${to},${base},${chunkn},${rgline}" >> $outcsv
+        from=$((to + 1))
+        ((to += 10000))
         ((chunkn++))
     done
 
-    if [ $from -le $ncontainers ]
-    then
-        echo $crampath,${crampath}.crai,${from},${ncontainers},${base},${chunkn},${rgline}
+    if [ $from -le $ncontainers ]; then
+        echo "${realcram},${realcrai},${from},${ncontainers},${base},${chunkn},${rgline}" >> $outcsv
         ((chunkn++))
     fi
-done
+
+    echo $chunkn
+}
+
+# Function to process a CRAM file
+process_cram_file() {
+    local cram=$1
+    local chunkn=$2
+    local outcsv=$3
+
+    local read_groups=$(samtools view -H "$cram" | grep '@RG' | awk '{for(i=1;i<=NF;i++){if($i ~ /^ID:/){print substr($i,4)}}}')
+    local num_read_groups=$(echo "$read_groups" | wc -w)
+
+    if [ "$num_read_groups" -gt 1 ]; then
+        # Multiple read groups: process each separately
+        for rg in $read_groups; do
+            local output_cram="$(basename "${cram%.cram}")_output_${rg}.cram"
+            samtools view -h -r "$rg" -o "$output_cram" "$cram"
+            samtools index "$output_cram"
+            chunkn=$(chunk_cram "$output_cram" "$chunkn" "$outcsv")
+        done
+    else
+        # Single read group or no read groups
+        chunkn=$(chunk_cram "$cram" "$chunkn" "$outcsv")
+    fi
+
+    echo $chunkn
+}
+
+#  /\_/\        /\_/\
+# ( o.o ) main ( o.o )
+#  > ^ <        > ^ <
+
+# Check if cram_path is provided
+if [ -z "$1" ]; then
+    echo "Usage: $0 <cram_path>"
+    exit 1
+fi
+
+cram_path=$1
+chunkn=0
+outcsv=$2
+
+# Loop through each CRAM file in the specified directory. cram cannot be the synlinked cram
+for cram in ${cram_path}/*.cram; do
+    realcram=$(readlink -f $cram)
+    chunkn=$(process_cram_file $realcram $chunkn $outcsv)
+done

modules/local/generate_cram_csv.nf

@@ -1,11 +1,8 @@
 process GENERATE_CRAM_CSV {
     tag "${meta.id}"
-    label 'process_low'
+    label 'process_tiny'
 
-    conda "bioconda::samtools=1.17"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' :
-        'biocontainers/samtools:1.17--h00cdaf9_0' }"
+    container 'quay.io/sanger-tol/cramfilter_bwamem2_minimap2_samtools_perl:0.001-c1'
 
     input:
     tuple val(meta), path(crampath)
@@ -17,7 +14,7 @@ process GENERATE_CRAM_CSV {
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    generate_cram_csv.sh $crampath >> ${prefix}_cram.csv
+    generate_cram_csv.sh $crampath ${prefix}_cram.csv
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

subworkflows/local/generate_maps.nf

@@ -48,6 +48,8 @@ workflow GENERATE_MAPS {
     )
     ch_versions         = ch_versions.mix( GENERATE_CRAM_CSV.out.versions )
 
+    GENERATE_CRAM_CSV.out.csv.view()
+
     //
     // LOGIC: make branches for different hic aligner.
     //