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7918 pharokka update stub #9055

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7918 pharokka update stub #9055

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23e1b0f
#7918 update pharokka/instaldatabases stub
shivangi-7 Sep 13, 2025
31029a5
#8887 update gatk4/haplotypecaller stub
shivangi-7 Sep 13, 2025
e20bf4b
#8888 update fcs/fcsadaptor stub
shivangi-7 Sep 13, 2025
360ec5c
#8888 update snapshots
shivangi-7 Sep 13, 2025
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1 change: 1 addition & 0 deletions modules/nf-core/fcs/fcsadaptor/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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2 changes: 1 addition & 1 deletion modules/nf-core/fcs/fcsadaptor/tests/main.nf.test
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Expand Up @@ -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],
Expand Down
7 changes: 4 additions & 3 deletions modules/nf-core/fcs/fcsadaptor/tests/main.nf.test.snap
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Expand Up @@ -75,17 +75,18 @@
"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",
"test.skipped_trims.jsonl"
]
],
"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": "2025-09-13T17:33:46.849193902"
},
"stub_versions": {
"content": [
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-core/gatk4/haplotypecaller/main.nf
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Expand Up @@ -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}

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4 changes: 1 addition & 3 deletions modules/nf-core/pharokka/installdatabases/main.nf
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Expand Up @@ -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
Expand Down Expand Up @@ -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
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10 changes: 5 additions & 5 deletions subworkflows/nf-core/fasta_clean_fcs/tests/main.nf.test.snap
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Expand Up @@ -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": [
Expand Down Expand Up @@ -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": [
Expand Down Expand Up @@ -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": [
Expand Down Expand Up @@ -239,4 +239,4 @@
},
"timestamp": "2025-05-18T18:25:01.262466302"
}
}
}
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