From 0734afc11565cb9d39f9e8c3740be758bd75efb5 Mon Sep 17 00:00:00 2001 From: bobturneruk Date: Thu, 15 Jan 2026 09:02:55 +0000 Subject: [PATCH 1/8] feat: Update output names --- README.md | 6 +++--- main.nf | 11 ++++++----- 2 files changed, 9 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index 914252a..5baf76b 100644 --- a/README.md +++ b/README.md @@ -42,16 +42,16 @@ work │   ├── outdir │   │   ├── alternate-cortex.vcf │   │   ├── alternate-samtools.vcf -│   │   ├── alternate.gvcf +│   │   ├── all_calls.gvcf │   │   ├── final.bam │   │   ├── final.bam.bai │   │   ├── final.fasta -│   │   ├── final.vcf +│   │   ├── variants.vcf │   │   └── genome_creation_error.json │   └── ref_data └── f3 └── a06ba84ace7c1185a462d5f549562a - ├── alternate.gvcf + ├── all_calls.gvcf ├── final.fasta ├── genome_creation_report.json ├── het_list diff --git a/main.nf b/main.nf index 0984d94..f4ea420 100644 --- a/main.nf +++ b/main.nf @@ -92,10 +92,10 @@ process run_clockwork { output: tuple val(sample_name), path("${outdir}/alternate-cortex.vcf.gz"), emit: cortex_vcf - tuple val(sample_name), path("${outdir}/alternate.gvcf.gz"), emit: final_gvcf - tuple val(sample_name), path("${outdir}/alternate.gvcf"), emit: final_gvcf_decompressed + tuple val(sample_name), path("${outdir}/all_calls.gvcf.gz"), emit: all_calls_gvcf + tuple val(sample_name), path("${outdir}/all_calls.gvcf"), emit: all_calls_gvcf_decompressed tuple val(sample_name), path("${outdir}/final.fasta"), emit: final_fasta - tuple val(sample_name), path("${outdir}/final.vcf"), emit: final_vcf + tuple val(sample_name), path("${outdir}/variants.vcf"), emit: variants_vcf tuple val(sample_name), path("${outdir}/alternate-samtools.vcf.gz"), emit: samtools_vcf tuple val(sample_name), path("${outdir}/final.bam"), emit: map_bam tuple val(sample_name), path("${outdir}/final.bam.bai"), emit: map_bam_bai @@ -109,9 +109,10 @@ process run_clockwork { echo -e "##fileformat=VCFv4.2\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tsample" > ${outdir}/cortex.vcf fi + mv ${outdir}/final.vcf ${outdir}/variants.vcf mv ${outdir}/cortex.vcf ${outdir}/alternate-cortex.vcf - mv ${outdir}/final.gvcf ${outdir}/alternate.gvcf - gzip -k ${outdir}/alternate.gvcf + mv ${outdir}/final.gvcf ${outdir}/all_calls.vcf + gzip -k ${outdir}/all_calls.vcf mv ${outdir}/final.gvcf.fasta ${outdir}/final.fasta mv ${outdir}/samtools.vcf ${outdir}/alternate-samtools.vcf mv ${outdir}/map.bam ${outdir}/final.bam From fdaf709615f4b5e16f728ce9830556abbfaa94be Mon Sep 17 00:00:00 2001 From: bobturneruk Date: Thu, 15 Jan 2026 09:04:54 +0000 Subject: [PATCH 2/8] docs: changelog file name changes --- CHANGELOG.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 262d47b..4a8ecbb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,9 @@ +## New + +- Update output file names: + - `final.vcf` to `variants.vcf` + - `alternate.gvcf` to `all_calls.vcf` + ## 1.0.1 - chore: Parameterise container prefix From 6f756c12514925bcf778a1b56e9dd687875f5f38 Mon Sep 17 00:00:00 2001 From: bobturneruk Date: Thu, 15 Jan 2026 09:07:07 +0000 Subject: [PATCH 3/8] fix: remove `g` from `gvcf` extension --- main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/main.nf b/main.nf index f4ea420..69b63e1 100644 --- a/main.nf +++ b/main.nf @@ -92,8 +92,8 @@ process run_clockwork { output: tuple val(sample_name), path("${outdir}/alternate-cortex.vcf.gz"), emit: cortex_vcf - tuple val(sample_name), path("${outdir}/all_calls.gvcf.gz"), emit: all_calls_gvcf - tuple val(sample_name), path("${outdir}/all_calls.gvcf"), emit: all_calls_gvcf_decompressed + tuple val(sample_name), path("${outdir}/all_calls.vcf.gz"), emit: all_calls_vcf + tuple val(sample_name), path("${outdir}/all_calls.vcf"), emit: all_calls_vcf_decompressed tuple val(sample_name), path("${outdir}/final.fasta"), emit: final_fasta tuple val(sample_name), path("${outdir}/variants.vcf"), emit: variants_vcf tuple val(sample_name), path("${outdir}/alternate-samtools.vcf.gz"), emit: samtools_vcf From 68e5e5d63dcbe2c1dbf3b562dbf9fa05b32d1cfc Mon Sep 17 00:00:00 2001 From: bobturneruk Date: Thu, 15 Jan 2026 09:08:20 +0000 Subject: [PATCH 4/8] fix: correct channel names in workflow --- main.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/main.nf b/main.nf index 69b63e1..27bb418 100644 --- a/main.nf +++ b/main.nf @@ -62,12 +62,12 @@ workflow clockwork { main: run_clockwork(reads, ref_files) - calc_counts(run_clockwork.out.final_gvcf.join(run_clockwork.out.final_fasta), "${moduleDir}/tb_clockwork_report.json.template", ref_files) + calc_counts(run_clockwork.out.all_calls_vcf.join(run_clockwork.out.final_fasta), "${moduleDir}/tb_clockwork_report.json.template", ref_files) emit: cortex_vcf = run_clockwork.out.cortex_vcf - final_gvcf = run_clockwork.out.final_gvcf - final_gvcf_decompressed = run_clockwork.out.final_gvcf_decompressed + all_calls_vcf = run_clockwork.out.all_calls_vcf + all_calls_vcf_decompressed = run_clockwork.out.all_calls_vcf_decompressed final_fasta = run_clockwork.out.final_fasta final_vcf = run_clockwork.out.final_vcf samtools_vcf = run_clockwork.out.samtools_vcf From 1254665eb08e2d431dca1eb8caab44fb017fa15d Mon Sep 17 00:00:00 2001 From: bobturneruk Date: Thu, 15 Jan 2026 09:10:26 +0000 Subject: [PATCH 5/8] fix: correct final to variants vcf in workflow --- main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main.nf b/main.nf index 27bb418..1bba524 100644 --- a/main.nf +++ b/main.nf @@ -69,7 +69,7 @@ workflow clockwork { all_calls_vcf = run_clockwork.out.all_calls_vcf all_calls_vcf_decompressed = run_clockwork.out.all_calls_vcf_decompressed final_fasta = run_clockwork.out.final_fasta - final_vcf = run_clockwork.out.final_vcf + variants_vcf = run_clockwork.out.variants_vcf samtools_vcf = run_clockwork.out.samtools_vcf map_bam = run_clockwork.out.map_bam map_bam_bai = run_clockwork.out.map_bam_bai From 940bfcc7f16a376363398daa0036b4675ce05d26 Mon Sep 17 00:00:00 2001 From: bobturneruk Date: Fri, 16 Jan 2026 11:39:33 +0000 Subject: [PATCH 6/8] test: check correct output files from workflow --- tests/workflow.nf.test | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/tests/workflow.nf.test b/tests/workflow.nf.test index 8c226ea..d1b8fcc 100644 --- a/tests/workflow.nf.test +++ b/tests/workflow.nf.test @@ -16,6 +16,10 @@ nextflow_workflow { then { assert workflow.success + assert workflow.out.final_fasta[0][1].contains('final.fasta') + assert workflow.out.variants_vcf[0][1].contains('variants.vcf') + assert workflow.out.all_calls_vcf[0][1].contains('all_calls.vcf') + assert path(workflow.out.final_fasta[0][1]).md5 == path("$projectDir/test_data/successful/expected_output.fasta").md5 assert path(workflow.out.cortex_vcf[0][1]).linesGzip != path("$projectDir/test_data/not_enough_reads/empty.vcf.gz").linesGzip } From ae8f5a7754af9e2b7d31df65b90060d8d3275efc Mon Sep 17 00:00:00 2001 From: "Robert (Bob) Turner" <34244196+bobturneruk@users.noreply.github.com> Date: Fri, 16 Jan 2026 12:31:33 +0000 Subject: [PATCH 7/8] docs: `gvcf` -> `vcf` Co-authored-by: JeremyWesthead <67918949+JeremyWesthead@users.noreply.github.com> --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 5baf76b..35549f1 100644 --- a/README.md +++ b/README.md @@ -51,7 +51,7 @@ work │   └── ref_data └── f3 └── a06ba84ace7c1185a462d5f549562a - ├── all_calls.gvcf + ├── all_calls.vcf ├── final.fasta ├── genome_creation_report.json ├── het_list From 6209844307fb81c80e58e627a9be536ef3bedb00 Mon Sep 17 00:00:00 2001 From: "Robert (Bob) Turner" <34244196+bobturneruk@users.noreply.github.com> Date: Fri, 16 Jan 2026 12:32:11 +0000 Subject: [PATCH 8/8] docs: `gvcf` -> `vcf` Co-authored-by: JeremyWesthead <67918949+JeremyWesthead@users.noreply.github.com> --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 35549f1..dcf283d 100644 --- a/README.md +++ b/README.md @@ -42,7 +42,7 @@ work │   ├── outdir │   │   ├── alternate-cortex.vcf │   │   ├── alternate-samtools.vcf -│   │   ├── all_calls.gvcf +│   │   ├── all_calls.vcf │   │   ├── final.bam │   │   ├── final.bam.bai │   │   ├── final.fasta