Nextflow 26.x compat and tabs→spaces in generatemutfasta

modules/msk/generatemutfasta/main.nf

@@ -27,10 +27,8 @@ process GENERATEMUTFASTA {
 
     tar -xzf ${mutalyzer_cache} -C \$(pwd)/mutalyzer_cache
 
-    cat <<-END_MUTALYZER_CONFIG > \$(pwd)/config.txt
-	MUTALYZER_CACHE_DIR = \$(pwd)/mutalyzer_cache/cache
-	MUTALYZER_FILE_CACHE_ADD = false
-	END_MUTALYZER_CONFIG
+    echo MUTALYZER_CACHE_DIR = \$(pwd)/mutalyzer_cache/cache >> \$(pwd)/config.txt
+    echo MUTALYZER_FILE_CACHE_ADD = false >> \$(pwd)/config.txt
 
     mkdir ${prefix}_out
 

subworkflows/msk/generate_mutated_peptides/main.nf

@@ -74,17 +74,17 @@ workflow GENERATE_MUTATED_PEPTIDES {
 }
 
 def createNEOSVInput(sv_bedpe, hla_str) {
-        sv_bedpe_channel = sv_bedpe
+        def sv_bedpe_channel = sv_bedpe
             .map{
                 new Tuple(it[0],it)
                 }
 
-        hla_str_channel = hla_str
+        def hla_str_channel = hla_str
             .map{
                 new Tuple(it[0],it)
                 }
 
-        merged_sv_hla = sv_bedpe_channel
+        def merged_sv_hla = sv_bedpe_channel
             .join(hla_str_channel, by:0)
             .map{
                 new Tuple(it[1][0], it[1][1], it[2][1])

subworkflows/msk/netmhcstabandpan/main.nf

@@ -48,27 +48,27 @@ workflow NETMHCSTABANDPAN {
 }
 
 def createNETMHCInput(fastas_and_hla, sv_fastas) {
-        fastas_and_hla_channel = fastas_and_hla
+        def fastas_and_hla_channel = fastas_and_hla
             .map{
                 new Tuple(it[0],it)
                 }
 
-        sv_fastas_channel = sv_fastas
+        def sv_fastas_channel = sv_fastas
             .map{
                 new Tuple(it[0],it)
                 }
 
-        merged_mut = fastas_and_hla_channel
+        def merged_mut = fastas_and_hla_channel
             .join(sv_fastas_channel, by:0)
             .map({
                 new Tuple(it[1][0], it[1][1], it[2][1], it[1][3], "MUT")
             })
 
-        merged_wt = fastas_and_hla_channel
+        def merged_wt = fastas_and_hla_channel
             .join(sv_fastas_channel, by:0)
             .map({
                 new Tuple(it[1][0], it[1][2], it[2][2], it[1][3], "WT")
             })
-        merged = merged_mut.mix(merged_wt)
+        def merged = merged_mut.mix(merged_wt)
         return merged
 }

subworkflows/msk/phylowgs/main.nf

@@ -50,17 +50,17 @@ workflow PHYLOWGS {
 }
 
 def join_maf_with_cnv(maf,cnv) {
-        maf_channel = maf
+        def maf_channel = maf
             .map{
                 new Tuple(it[0].id,it)
                 }
-        cnv_channel = cnv
+        def cnv_channel = cnv
             .map{
                 new Tuple(it[0].id,it)
                 }
-        mergedWithKey = maf_channel
+        def mergedWithKey = maf_channel
             .join(cnv_channel)
-        merged = mergedWithKey
+        def merged = mergedWithKey
             .map{
                 new Tuple(it[1][0],it[1][1],it[2][1])
             }