From d35b9a4daac9625e3b2b87466336edf5d0abe380 Mon Sep 17 00:00:00 2001 From: John Orgera <65687576+johnoooh@users.noreply.github.com> Date: Fri, 13 Feb 2026 11:48:27 -0500 Subject: [PATCH 1/3] =?UTF-8?q?Fix=20Nextflow=2026.x=20compat:=20tabs?= =?UTF-8?q?=E2=86=92spaces=20in=20generatemutfasta,=20add=20def=20to=20sub?= =?UTF-8?q?workflow=20vars?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - generatemutfasta/main.nf: Convert tab indentation to spaces in END_MUTALYZER_CONFIG heredoc to fix YAML runtime error caused by mixed tab/space indentation with stripIndent() - generate_mutated_peptides/main.nf: Add def to 3 local vars in createNEOSVInput() - netmhcstabandpan/main.nf: Add def to 5 local vars in createNETMHCInput() - phylowgs/main.nf: Add def to 4 local vars in join_maf_with_cnv() Co-Authored-By: Claude Opus 4.6 --- modules/msk/generatemutfasta/main.nf | 6 +++--- subworkflows/msk/generate_mutated_peptides/main.nf | 6 +++--- subworkflows/msk/netmhcstabandpan/main.nf | 10 +++++----- subworkflows/msk/phylowgs/main.nf | 8 ++++---- 4 files changed, 15 insertions(+), 15 deletions(-) diff --git a/modules/msk/generatemutfasta/main.nf b/modules/msk/generatemutfasta/main.nf index bc4526dd..4eafa0a0 100644 --- a/modules/msk/generatemutfasta/main.nf +++ b/modules/msk/generatemutfasta/main.nf @@ -28,9 +28,9 @@ 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 + MUTALYZER_CACHE_DIR = \$(pwd)/mutalyzer_cache/cache + MUTALYZER_FILE_CACHE_ADD = false + END_MUTALYZER_CONFIG mkdir ${prefix}_out diff --git a/subworkflows/msk/generate_mutated_peptides/main.nf b/subworkflows/msk/generate_mutated_peptides/main.nf index 0ddc05ee..610ee13b 100644 --- a/subworkflows/msk/generate_mutated_peptides/main.nf +++ b/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]) diff --git a/subworkflows/msk/netmhcstabandpan/main.nf b/subworkflows/msk/netmhcstabandpan/main.nf index 805e89cc..b82fdfcf 100644 --- a/subworkflows/msk/netmhcstabandpan/main.nf +++ b/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 } diff --git a/subworkflows/msk/phylowgs/main.nf b/subworkflows/msk/phylowgs/main.nf index f15f272b..bbf502b5 100644 --- a/subworkflows/msk/phylowgs/main.nf +++ b/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]) } From 18a47f61d6bfdb4fc4a0a042b27d17f9d809bd1b Mon Sep 17 00:00:00 2001 From: Nikhil Kumar Date: Fri, 13 Feb 2026 12:14:07 -0500 Subject: [PATCH 2/3] Fixed here doc From 3857da5a6eb17ddeaef6d1bd1842c843d76d437a Mon Sep 17 00:00:00 2001 From: Nikhil Kumar Date: Fri, 13 Feb 2026 12:33:12 -0500 Subject: [PATCH 3/3] Remove mutalyzer config heredoc --- modules/msk/generatemutfasta/main.nf | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/modules/msk/generatemutfasta/main.nf b/modules/msk/generatemutfasta/main.nf index 4eafa0a0..7d4588aa 100644 --- a/modules/msk/generatemutfasta/main.nf +++ b/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