From 23e1b0f1e7b4decb083b82ecd22323dd2a49ff2d Mon Sep 17 00:00:00 2001 From: Shivangi Verma Date: Sat, 13 Sep 2025 15:58:38 +0000 Subject: [PATCH 1/4] #7918 update pharokka/instaldatabases stub --- modules/nf-core/pharokka/installdatabases/main.nf | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/modules/nf-core/pharokka/installdatabases/main.nf b/modules/nf-core/pharokka/installdatabases/main.nf index 132ff09d63e1..8bf6dd0840a3 100644 --- a/modules/nf-core/pharokka/installdatabases/main.nf +++ b/modules/nf-core/pharokka/installdatabases/main.nf @@ -6,8 +6,6 @@ process PHAROKKA_INSTALLDATABASES { 'https://depot.galaxyproject.org/singularity/pharokka:1.7.3--pyhdfd78af_0': 'biocontainers/pharokka:1.7.3--pyhdfd78af_0' }" - input: - output: path("${prefix}/") , emit: pharokka_db path "versions.yml" , emit: versions @@ -44,7 +42,7 @@ process PHAROKKA_INSTALLDATABASES { touch $prefix/CARD_h touch $prefix/CARD_h.dbtype touch $prefix/CARD_h.index - touch $prefix/VFDB_setB_pro.fas.gz + echo | gzip > $prefix/VFDB_setB_pro.fas.gz touch $prefix/VFDBclusterRes_cluster.tsv touch $prefix/VFDBclusterRes_rep_seq.fasta touch $prefix/all_phrogs.h3m From 31029a5b28d13a5418ace05b155dc15bedfdf658 Mon Sep 17 00:00:00 2001 From: Shivangi Verma Date: Sat, 13 Sep 2025 16:48:34 +0000 Subject: [PATCH 2/4] #8887 update gatk4/haplotypecaller stub --- modules/nf-core/gatk4/haplotypecaller/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index 3ab550262eec..f6932796153d 100644 --- a/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -66,7 +66,7 @@ process GATK4_HAPLOTYPECALLER { def stub_realigned_bam = bamout_command ? "touch ${prefix.replaceAll('.g\\s*$', '')}.realigned.bam" : "" """ - touch ${prefix}.vcf.gz + echo | gzip > ${prefix}.vcf.gz touch ${prefix}.vcf.gz.tbi ${stub_realigned_bam} From e20bf4b8f5ca7717c28d0a2ab75a6b406d0204d1 Mon Sep 17 00:00:00 2001 From: Shivangi Verma Date: Sat, 13 Sep 2025 17:11:05 +0000 Subject: [PATCH 3/4] #8888 update fcs/fcsadaptor stub --- modules/nf-core/fcs/fcsadaptor/main.nf | 1 + modules/nf-core/fcs/fcsadaptor/tests/main.nf.test.snap | 7 ++++--- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/fcs/fcsadaptor/main.nf b/modules/nf-core/fcs/fcsadaptor/main.nf index a69c99f1e5a5..770a4d929cf8 100644 --- a/modules/nf-core/fcs/fcsadaptor/main.nf +++ b/modules/nf-core/fcs/fcsadaptor/main.nf @@ -79,6 +79,7 @@ process FCS_FCSADAPTOR { def FCSADAPTOR_VERSION = '0.5.0' """ + echo | gzip > ${prefix}.cleaned_sequences.fa.gz touch ${prefix}.fcs_adaptor_report.txt touch ${prefix}.fcs_adaptor.log touch ${prefix}.pipeline_args.yaml diff --git a/modules/nf-core/fcs/fcsadaptor/tests/main.nf.test.snap b/modules/nf-core/fcs/fcsadaptor/tests/main.nf.test.snap index ca3975ee2ba0..c3b176724bb1 100644 --- a/modules/nf-core/fcs/fcsadaptor/tests/main.nf.test.snap +++ b/modules/nf-core/fcs/fcsadaptor/tests/main.nf.test.snap @@ -75,6 +75,7 @@ "bacteroides_fragilis-genome_fna_gz-stub": { "content": [ [ + "test.cleaned_sequences.fa.gz", "test.fcs_adaptor_report.txt", "test.fcs_adaptor.log", "test.pipeline_args.yaml", @@ -82,10 +83,10 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "25.04.6" }, - "timestamp": "2024-05-09T11:51:58.777173" + "timestamp": "2025-09-13T17:05:30.788576882" }, "stub_versions": { "content": [ From 360ec5c31045e5156697b7685f156174ebab1a1f Mon Sep 17 00:00:00 2001 From: Shivangi Verma Date: Sat, 13 Sep 2025 17:41:24 +0000 Subject: [PATCH 4/4] #8888 update snapshots --- modules/nf-core/fcs/fcsadaptor/tests/main.nf.test | 2 +- modules/nf-core/fcs/fcsadaptor/tests/main.nf.test.snap | 2 +- .../nf-core/fasta_clean_fcs/tests/main.nf.test.snap | 10 +++++----- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/modules/nf-core/fcs/fcsadaptor/tests/main.nf.test b/modules/nf-core/fcs/fcsadaptor/tests/main.nf.test index 13caaceabb4a..201bdda96bd4 100644 --- a/modules/nf-core/fcs/fcsadaptor/tests/main.nf.test +++ b/modules/nf-core/fcs/fcsadaptor/tests/main.nf.test @@ -98,9 +98,9 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert process.out.cleaned_assembly == [] }, { assert snapshot( [ + process.out.cleaned_assembly[0][1], process.out.adaptor_report[0][1], process.out.log[0][1], process.out.pipeline_args[0][1], diff --git a/modules/nf-core/fcs/fcsadaptor/tests/main.nf.test.snap b/modules/nf-core/fcs/fcsadaptor/tests/main.nf.test.snap index c3b176724bb1..a0b7ee03ad9b 100644 --- a/modules/nf-core/fcs/fcsadaptor/tests/main.nf.test.snap +++ b/modules/nf-core/fcs/fcsadaptor/tests/main.nf.test.snap @@ -86,7 +86,7 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-13T17:05:30.788576882" + "timestamp": "2025-09-13T17:33:46.849193902" }, "stub_versions": { "content": [ diff --git a/subworkflows/nf-core/fasta_clean_fcs/tests/main.nf.test.snap b/subworkflows/nf-core/fasta_clean_fcs/tests/main.nf.test.snap index 7f839632f047..6bad22578961 100644 --- a/subworkflows/nf-core/fasta_clean_fcs/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fasta_clean_fcs/tests/main.nf.test.snap @@ -9,7 +9,7 @@ "taxid": "9606" }, "9606", - "/nf-core/test-datasets/modules/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz" + "test.cleaned_sequences.fa.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "1": [ @@ -95,7 +95,7 @@ "taxid": "9606" }, "9606", - "/nf-core/test-datasets/modules/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz" + "test.cleaned_sequences.fa.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "fcsadaptor_log": [ @@ -190,9 +190,9 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.5" + "nextflow": "25.04.6" }, - "timestamp": "2025-05-18T17:35:00.532976534" + "timestamp": "2025-09-13T17:39:45.310992465" }, "bacteroides_fragilis - fna - gwi gws taxa jsonl blast_div": { "content": [ @@ -239,4 +239,4 @@ }, "timestamp": "2025-05-18T18:25:01.262466302" } -} +} \ No newline at end of file