From 87901781fc039912abe623ea56bdb8c64b224a1b Mon Sep 17 00:00:00 2001 From: Sofia Stamouli Date: Fri, 28 Jul 2023 17:18:53 +0200 Subject: [PATCH 01/21] Update kmcp profile --- modules/nf-core/kmcp/profile/main.nf | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/kmcp/profile/main.nf b/modules/nf-core/kmcp/profile/main.nf index cc520ef8907..a46721224b1 100644 --- a/modules/nf-core/kmcp/profile/main.nf +++ b/modules/nf-core/kmcp/profile/main.nf @@ -9,8 +9,7 @@ process KMCP_PROFILE { input: tuple val(meta), path(search_results) - path taxdump - path taxid + path (db) val mode output: @@ -24,11 +23,13 @@ process KMCP_PROFILE { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ + taxid=`find -L ${db} -name "*map"` + taxdump=`find -L ${db}/*/ -type d -not -name "R001"` kmcp \\ profile \\ $args \\ - -X $taxdump \\ - -T $taxid \\ + -X \$taxdump \\ + -T \$taxid \\ -m $mode \\ -j $task.cpus \\ -o ${prefix}.profile \\ From 0c74302c986dbcb818349797382ba1ef66f659e4 Mon Sep 17 00:00:00 2001 From: Sofia Stamouli Date: Mon, 31 Jul 2023 16:15:28 +0200 Subject: [PATCH 02/21] Update kmcp modules --- tests/modules/nf-core/kmcp/compute/main.nf | 2 +- tests/modules/nf-core/kmcp/compute/test.yml | 2 +- tests/modules/nf-core/kmcp/profile/main.nf | 16 +++++++--------- .../modules/nf-core/kmcp/profile/nextflow.config | 2 +- .../modules/nf-core/kmcp/search/nextflow.config | 4 ---- 5 files changed, 10 insertions(+), 16 deletions(-) diff --git a/tests/modules/nf-core/kmcp/compute/main.nf b/tests/modules/nf-core/kmcp/compute/main.nf index 73679ebae12..59860296890 100644 --- a/tests/modules/nf-core/kmcp/compute/main.nf +++ b/tests/modules/nf-core/kmcp/compute/main.nf @@ -19,7 +19,7 @@ workflow test_kmcp_compute_directory { input = UNTAR ( [ [ id:'test' ], - file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kmcp.tar.gz", checkIfExists: true) + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/kmcp/kmcp_profile.tar.gz", checkIfExists: true) ]).untar KMCP_COMPUTE ( input ) diff --git a/tests/modules/nf-core/kmcp/compute/test.yml b/tests/modules/nf-core/kmcp/compute/test.yml index e10ea1c2873..fc729f76a3e 100644 --- a/tests/modules/nf-core/kmcp/compute/test.yml +++ b/tests/modules/nf-core/kmcp/compute/test.yml @@ -1,8 +1,8 @@ - name: kmcp compute test_kmcp_compute command: nextflow run ./tests/modules/nf-core/kmcp/compute -entry test_kmcp_compute -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/kmcp/compute/nextflow.config tags: - - kmcp - kmcp/compute + - kmcp files: - path: output/kmcp/test_/_info.txt contains: ["#path name chunkIdx idxNum genomeSize kmers"] diff --git a/tests/modules/nf-core/kmcp/profile/main.nf b/tests/modules/nf-core/kmcp/profile/main.nf index e41f4a2a7c1..bed70144213 100644 --- a/tests/modules/nf-core/kmcp/profile/main.nf +++ b/tests/modules/nf-core/kmcp/profile/main.nf @@ -10,23 +10,21 @@ include { KMCP_PROFILE } from '../../../../../modules/nf-core/kmcp/profile/main. workflow test_kmcp_profile { - input_compute = [ - [ id:'test', single_end:false ], // meta map - file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kmcp/NC_045512.2.fasta', checkIfExists: true) - ] + input_compute= UNTAR ( [ + [ id:'test' ], + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/kmcp/kmcp_profile.tar.gz", checkIfExists: true) + ]).untar + input = [ [ id:'test', single_end:true ], // meta map file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] - taxdump = [ [],file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kmcp/kmcp_profile.tar.gz', checkIfExists: true)] - ch_taxid = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/kmcp/seqid2taxid.map', checkIfExists: true) mode = 3 - UNTAR (taxdump) - KMCP_COMPUTE ( input_compute ) + KMCP_COMPUTE (input_compute ) KMCP_INDEX ( KMCP_COMPUTE.out.outdir ) KMCP_SEARCH ( KMCP_INDEX.out.kmcp.map{it[1]}, input ) - KMCP_PROFILE ( KMCP_SEARCH.out.result, UNTAR.out.untar.map{ it[1] }, ch_taxid, mode ) + KMCP_PROFILE ( KMCP_SEARCH.out.result, input_compute.map{ it[1] }, mode ) } diff --git a/tests/modules/nf-core/kmcp/profile/nextflow.config b/tests/modules/nf-core/kmcp/profile/nextflow.config index dafa8f3f73f..98a493be45f 100644 --- a/tests/modules/nf-core/kmcp/profile/nextflow.config +++ b/tests/modules/nf-core/kmcp/profile/nextflow.config @@ -2,7 +2,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: KMCP_INDEX { + withName: KMCP_COMPUTE { ext.prefix = { "${meta.id}_" } } diff --git a/tests/modules/nf-core/kmcp/search/nextflow.config b/tests/modules/nf-core/kmcp/search/nextflow.config index 4eb081d2033..dafa8f3f73f 100644 --- a/tests/modules/nf-core/kmcp/search/nextflow.config +++ b/tests/modules/nf-core/kmcp/search/nextflow.config @@ -6,8 +6,4 @@ process { ext.prefix = { "${meta.id}_" } } - withName: KMCP_SEARCH { - ext.prefix = { "${meta.id}_" } - } - } From aa2f03f12814eaacfea9df2876686237fa662db0 Mon Sep 17 00:00:00 2001 From: Sofia Stamouli Date: Mon, 31 Jul 2023 16:26:24 +0200 Subject: [PATCH 03/21] Remove one line --- tests/modules/nf-core/kmcp/compute/test.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/modules/nf-core/kmcp/compute/test.yml b/tests/modules/nf-core/kmcp/compute/test.yml index fc729f76a3e..a8dbb2a24ee 100644 --- a/tests/modules/nf-core/kmcp/compute/test.yml +++ b/tests/modules/nf-core/kmcp/compute/test.yml @@ -27,5 +27,4 @@ - path: output/kmcp/test_/_info.txt contains: ["#path name chunkIdx idxNum genomeSize kmers"] - path: output/kmcp/test_/genome.fasta.unik - - path: output/kmcp/test_/transcriptome.fasta.unik - path: output/kmcp/versions.yml From d90b7a37b5f929c6ef74c98ee2765a076431b6e3 Mon Sep 17 00:00:00 2001 From: Sofia Stamouli Date: Mon, 31 Jul 2023 16:37:07 +0200 Subject: [PATCH 04/21] Update test.yml for kmcp/profile --- tests/modules/nf-core/kmcp/profile/test.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/modules/nf-core/kmcp/profile/test.yml b/tests/modules/nf-core/kmcp/profile/test.yml index 4d537bbd5ea..77f6570ff55 100644 --- a/tests/modules/nf-core/kmcp/profile/test.yml +++ b/tests/modules/nf-core/kmcp/profile/test.yml @@ -1,11 +1,11 @@ - name: kmcp profile test_kmcp_profile command: nextflow run ./tests/modules/nf-core/kmcp/profile -entry test_kmcp_profile -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/kmcp/profile/nextflow.config tags: - - kmcp/profile - kmcp + - kmcp/profile files: - path: output/kmcp/test.profile - - path: output/untar/versions.yml + - path: output/kmcp/versions.yml - name: kmcp profile test_kmcp_profile stub_run command: nextflow run ./tests/modules/nf-core/kmcp/profile -entry test_kmcp_profile -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/kmcp/profile/nextflow.config -stub-run @@ -14,4 +14,4 @@ - kmcp files: - path: output/kmcp/test.profile - - path: output/untar/versions.yml + - path: output/kmcp/versions.yml From 97cffe070934da13519ad8834bf341e3a8075a49 Mon Sep 17 00:00:00 2001 From: Sofia Stamouli Date: Mon, 31 Jul 2023 16:50:10 +0200 Subject: [PATCH 05/21] test.yml --- tests/modules/nf-core/kmcp/profile/test.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/tests/modules/nf-core/kmcp/profile/test.yml b/tests/modules/nf-core/kmcp/profile/test.yml index 77f6570ff55..247a42d8dbc 100644 --- a/tests/modules/nf-core/kmcp/profile/test.yml +++ b/tests/modules/nf-core/kmcp/profile/test.yml @@ -4,6 +4,7 @@ - kmcp - kmcp/profile files: + - path: output/kmcp/test.gz - path: output/kmcp/test.profile - path: output/kmcp/versions.yml @@ -13,5 +14,6 @@ - kmcp/profile - kmcp files: + - path: output/kmcp/test.gz - path: output/kmcp/test.profile - - path: output/kmcp/versions.yml + - path: output/untar/versions.yml From 24af23f6272aa741ba061da1ebfa34e155e1565e Mon Sep 17 00:00:00 2001 From: Sofia Stamouli Date: Mon, 31 Jul 2023 17:18:46 +0200 Subject: [PATCH 06/21] Fix linting --- modules/nf-core/kmcp/profile/meta.yml | 11 +++-------- tests/config/pytest_modules.yml | 8 ++++++++ 2 files changed, 11 insertions(+), 8 deletions(-) diff --git a/modules/nf-core/kmcp/profile/meta.yml b/modules/nf-core/kmcp/profile/meta.yml index 512a882eab4..14f292c758e 100644 --- a/modules/nf-core/kmcp/profile/meta.yml +++ b/modules/nf-core/kmcp/profile/meta.yml @@ -23,18 +23,13 @@ input: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] + - db: + type: directory + description: Database directory containing taxdump files and taxid file - search_results: type: file description: Gzipped file output from kmcp search module pattern: "*.gz" - - taxdump: - type: directory - description: Directory of NCBI taxonomy dump files - names.dmp, nodes.dmp - pattern: "*" - - taxid: - type: file - description: Tabular two-column file(s) mapping reference IDs to TaxIds. - pattern: "*.{csv,tsv}" - mode: type: integer description: Profiling mode. diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 39a14960902..7b285ab12e0 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -2045,10 +2045,18 @@ kmcp/index: - modules/nf-core/kmcp/index/** - tests/modules/nf-core/kmcp/index/** +kmcp/merge: + - modules/nf-core/kmcp/merge/** + - tests/modules/nf-core/kmcp/merge/** + kmcp/profile: - modules/nf-core/kmcp/profile/** - tests/modules/nf-core/kmcp/profile/** +kmcp/search: + - modules/nf-core/kmcp/search/** + - tests/modules/nf-core/kmcp/search/** + kofamscan: - modules/nf-core/kofamscan/** - tests/modules/nf-core/kofamscan/** From 6b1b4896cab36f1f93ba356634ded8a6582fa2fc Mon Sep 17 00:00:00 2001 From: Sofia Stamouli Date: Mon, 31 Jul 2023 17:24:57 +0200 Subject: [PATCH 07/21] Update to kmcp:0.9.3 --- modules/nf-core/kmcp/compute/main.nf | 4 ++-- modules/nf-core/kmcp/index/main.nf | 4 ++-- modules/nf-core/kmcp/merge/main.nf | 4 ++-- modules/nf-core/kmcp/profile/main.nf | 4 ++-- modules/nf-core/kmcp/search/main.nf | 4 ++-- 5 files changed, 10 insertions(+), 10 deletions(-) diff --git a/modules/nf-core/kmcp/compute/main.nf b/modules/nf-core/kmcp/compute/main.nf index 2e4458f4d9b..f8fb9cd9e89 100644 --- a/modules/nf-core/kmcp/compute/main.nf +++ b/modules/nf-core/kmcp/compute/main.nf @@ -4,8 +4,8 @@ process KMCP_COMPUTE { conda "bioconda::kmcp=0.9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/kmcp:0.9.1--h9ee0642_0': - 'biocontainers/kmcp:0.9.1--h9ee0642_0' }" + 'https://depot.galaxyproject.org/singularity/kmcp:0.9.3--h9ee0642_0': + 'biocontainers/kmcp:0.9.3--h9ee0642_0' }" input: tuple val(meta), path(sequences) diff --git a/modules/nf-core/kmcp/index/main.nf b/modules/nf-core/kmcp/index/main.nf index 6a06b98acb8..2f8da8afcaa 100644 --- a/modules/nf-core/kmcp/index/main.nf +++ b/modules/nf-core/kmcp/index/main.nf @@ -4,8 +4,8 @@ process KMCP_INDEX { conda "bioconda::kmcp=0.9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/kmcp:0.9.1--h9ee0642_0': - 'quay.io/biocontainers/kmcp:0.9.1--h9ee0642_0' }" + 'https://depot.galaxyproject.org/singularity/kmcp:0.9.3--h9ee0642_0': + 'quay.io/biocontainers/kmcp:0.9.3--h9ee0642_0' }" input: tuple val(meta), path(compute_dir) diff --git a/modules/nf-core/kmcp/merge/main.nf b/modules/nf-core/kmcp/merge/main.nf index a53fecdc5c7..ffa78f3885a 100644 --- a/modules/nf-core/kmcp/merge/main.nf +++ b/modules/nf-core/kmcp/merge/main.nf @@ -5,8 +5,8 @@ process KMCP_MERGE { conda "bioconda::kmcp=0.9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/kmcp:0.9.1--h9ee0642_0': - 'quay.io/biocontainers/kmcp:0.9.1--h9ee0642_0' }" + 'https://depot.galaxyproject.org/singularity/kmcp:0.9.3--h9ee0642_0': + 'quay.io/biocontainers/kmcp:0.9.3--h9ee0642_0' }" input: diff --git a/modules/nf-core/kmcp/profile/main.nf b/modules/nf-core/kmcp/profile/main.nf index a46721224b1..7cdc3fccc34 100644 --- a/modules/nf-core/kmcp/profile/main.nf +++ b/modules/nf-core/kmcp/profile/main.nf @@ -4,8 +4,8 @@ process KMCP_PROFILE { conda "bioconda::kmcp=0.9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/kmcp:0.9.1--h9ee0642_0': - 'biocontainers/kmcp:0.9.1--h9ee0642_0' }" + 'https://depot.galaxyproject.org/singularity/kmcp:0.9.3--h9ee0642_0': + 'biocontainers/kmcp:0.9.3--h9ee0642_0' }" input: tuple val(meta), path(search_results) diff --git a/modules/nf-core/kmcp/search/main.nf b/modules/nf-core/kmcp/search/main.nf index b0b5e960406..79285c9c91f 100644 --- a/modules/nf-core/kmcp/search/main.nf +++ b/modules/nf-core/kmcp/search/main.nf @@ -4,8 +4,8 @@ process KMCP_SEARCH { conda "bioconda::kmcp=0.9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/kmcp:0.9.1--h9ee0642_0': - 'biocontainers/kmcp:0.9.1--h9ee0642_0' }" + 'https://depot.galaxyproject.org/singularity/kmcp:0.9.3--h9ee0642_0': + 'biocontainers/kmcp:0.9.3--h9ee0642_0' }" input: path(db) From be4fb5f3bb794c710f07c77f8ec5cc938f517231 Mon Sep 17 00:00:00 2001 From: Sofia Stamouli Date: Mon, 31 Jul 2023 17:30:49 +0200 Subject: [PATCH 08/21] kmcp=0.9.3 --- modules/nf-core/kmcp/compute/main.nf | 2 +- modules/nf-core/kmcp/index/main.nf | 2 +- modules/nf-core/kmcp/profile/main.nf | 2 +- modules/nf-core/kmcp/search/main.nf | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/kmcp/compute/main.nf b/modules/nf-core/kmcp/compute/main.nf index f8fb9cd9e89..b07710f029a 100644 --- a/modules/nf-core/kmcp/compute/main.nf +++ b/modules/nf-core/kmcp/compute/main.nf @@ -2,7 +2,7 @@ process KMCP_COMPUTE { tag "$meta.id" label 'process_medium' - conda "bioconda::kmcp=0.9.1" + conda "bioconda::kmcp=0.9.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kmcp:0.9.3--h9ee0642_0': 'biocontainers/kmcp:0.9.3--h9ee0642_0' }" diff --git a/modules/nf-core/kmcp/index/main.nf b/modules/nf-core/kmcp/index/main.nf index 2f8da8afcaa..ad285233527 100644 --- a/modules/nf-core/kmcp/index/main.nf +++ b/modules/nf-core/kmcp/index/main.nf @@ -2,7 +2,7 @@ process KMCP_INDEX { tag "$meta.id" label 'process_medium' - conda "bioconda::kmcp=0.9.1" + conda "bioconda::kmcp=0.9.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kmcp:0.9.3--h9ee0642_0': 'quay.io/biocontainers/kmcp:0.9.3--h9ee0642_0' }" diff --git a/modules/nf-core/kmcp/profile/main.nf b/modules/nf-core/kmcp/profile/main.nf index 7cdc3fccc34..3a9ea9bc65b 100644 --- a/modules/nf-core/kmcp/profile/main.nf +++ b/modules/nf-core/kmcp/profile/main.nf @@ -2,7 +2,7 @@ process KMCP_PROFILE { tag "$meta.id" label 'process_medium' - conda "bioconda::kmcp=0.9.1" + conda "bioconda::kmcp=0.9.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kmcp:0.9.3--h9ee0642_0': 'biocontainers/kmcp:0.9.3--h9ee0642_0' }" diff --git a/modules/nf-core/kmcp/search/main.nf b/modules/nf-core/kmcp/search/main.nf index 79285c9c91f..7ec45667981 100644 --- a/modules/nf-core/kmcp/search/main.nf +++ b/modules/nf-core/kmcp/search/main.nf @@ -2,7 +2,7 @@ process KMCP_SEARCH { tag "$meta.id" label 'process_medium' - conda "bioconda::kmcp=0.9.1" + conda "bioconda::kmcp=0.9.3" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/kmcp:0.9.3--h9ee0642_0': 'biocontainers/kmcp:0.9.3--h9ee0642_0' }" From 36cad67d718cda68c96ac38bc31497db63417c1c Mon Sep 17 00:00:00 2001 From: Sofia Stamouli Date: Mon, 31 Jul 2023 17:41:40 +0200 Subject: [PATCH 09/21] Version 0.9.1 --- modules/nf-core/kmcp/compute/main.nf | 6 +++--- modules/nf-core/kmcp/index/main.nf | 6 +++--- modules/nf-core/kmcp/merge/main.nf | 4 ++-- modules/nf-core/kmcp/profile/main.nf | 6 +++--- modules/nf-core/kmcp/search/main.nf | 6 +++--- 5 files changed, 14 insertions(+), 14 deletions(-) diff --git a/modules/nf-core/kmcp/compute/main.nf b/modules/nf-core/kmcp/compute/main.nf index b07710f029a..2e4458f4d9b 100644 --- a/modules/nf-core/kmcp/compute/main.nf +++ b/modules/nf-core/kmcp/compute/main.nf @@ -2,10 +2,10 @@ process KMCP_COMPUTE { tag "$meta.id" label 'process_medium' - conda "bioconda::kmcp=0.9.3" + conda "bioconda::kmcp=0.9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/kmcp:0.9.3--h9ee0642_0': - 'biocontainers/kmcp:0.9.3--h9ee0642_0' }" + 'https://depot.galaxyproject.org/singularity/kmcp:0.9.1--h9ee0642_0': + 'biocontainers/kmcp:0.9.1--h9ee0642_0' }" input: tuple val(meta), path(sequences) diff --git a/modules/nf-core/kmcp/index/main.nf b/modules/nf-core/kmcp/index/main.nf index ad285233527..6a06b98acb8 100644 --- a/modules/nf-core/kmcp/index/main.nf +++ b/modules/nf-core/kmcp/index/main.nf @@ -2,10 +2,10 @@ process KMCP_INDEX { tag "$meta.id" label 'process_medium' - conda "bioconda::kmcp=0.9.3" + conda "bioconda::kmcp=0.9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/kmcp:0.9.3--h9ee0642_0': - 'quay.io/biocontainers/kmcp:0.9.3--h9ee0642_0' }" + 'https://depot.galaxyproject.org/singularity/kmcp:0.9.1--h9ee0642_0': + 'quay.io/biocontainers/kmcp:0.9.1--h9ee0642_0' }" input: tuple val(meta), path(compute_dir) diff --git a/modules/nf-core/kmcp/merge/main.nf b/modules/nf-core/kmcp/merge/main.nf index ffa78f3885a..a53fecdc5c7 100644 --- a/modules/nf-core/kmcp/merge/main.nf +++ b/modules/nf-core/kmcp/merge/main.nf @@ -5,8 +5,8 @@ process KMCP_MERGE { conda "bioconda::kmcp=0.9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/kmcp:0.9.3--h9ee0642_0': - 'quay.io/biocontainers/kmcp:0.9.3--h9ee0642_0' }" + 'https://depot.galaxyproject.org/singularity/kmcp:0.9.1--h9ee0642_0': + 'quay.io/biocontainers/kmcp:0.9.1--h9ee0642_0' }" input: diff --git a/modules/nf-core/kmcp/profile/main.nf b/modules/nf-core/kmcp/profile/main.nf index 3a9ea9bc65b..a46721224b1 100644 --- a/modules/nf-core/kmcp/profile/main.nf +++ b/modules/nf-core/kmcp/profile/main.nf @@ -2,10 +2,10 @@ process KMCP_PROFILE { tag "$meta.id" label 'process_medium' - conda "bioconda::kmcp=0.9.3" + conda "bioconda::kmcp=0.9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/kmcp:0.9.3--h9ee0642_0': - 'biocontainers/kmcp:0.9.3--h9ee0642_0' }" + 'https://depot.galaxyproject.org/singularity/kmcp:0.9.1--h9ee0642_0': + 'biocontainers/kmcp:0.9.1--h9ee0642_0' }" input: tuple val(meta), path(search_results) diff --git a/modules/nf-core/kmcp/search/main.nf b/modules/nf-core/kmcp/search/main.nf index 7ec45667981..b0b5e960406 100644 --- a/modules/nf-core/kmcp/search/main.nf +++ b/modules/nf-core/kmcp/search/main.nf @@ -2,10 +2,10 @@ process KMCP_SEARCH { tag "$meta.id" label 'process_medium' - conda "bioconda::kmcp=0.9.3" + conda "bioconda::kmcp=0.9.1" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/kmcp:0.9.3--h9ee0642_0': - 'biocontainers/kmcp:0.9.3--h9ee0642_0' }" + 'https://depot.galaxyproject.org/singularity/kmcp:0.9.1--h9ee0642_0': + 'biocontainers/kmcp:0.9.1--h9ee0642_0' }" input: path(db) From 5d0e1394b471980a55601fe263cd4e2e46e1a574 Mon Sep 17 00:00:00 2001 From: Sofia Stamouli Date: Mon, 31 Jul 2023 17:53:13 +0200 Subject: [PATCH 10/21] Update test.yml for kmcp/search --- tests/modules/nf-core/kmcp/search/test.yml | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/tests/modules/nf-core/kmcp/search/test.yml b/tests/modules/nf-core/kmcp/search/test.yml index eb356e8755e..11ae4301b92 100644 --- a/tests/modules/nf-core/kmcp/search/test.yml +++ b/tests/modules/nf-core/kmcp/search/test.yml @@ -4,9 +4,7 @@ - kmcp - kmcp/search files: - - path: output/kmcp/test_/R001/__db.yml - - path: output/kmcp/test_/R001/__name_mapping.tsv - - path: output/kmcp/test_/R001/_block001.uniki + - path: output/kmcp/test.gz - path: output/kmcp/versions.yml - name: kmcp search test_kmcp_search stub_run @@ -15,7 +13,6 @@ - kmcp - kmcp/search files: - - path: output/kmcp/test_/R001/__db.yml - - path: output/kmcp/test_/R001/__name_mapping.tsv - - path: output/kmcp/test_/R001/_block001.uniki + - path: output/kmcp/test.gz - path: output/kmcp/versions.yml + From cd546fa1c8b805f599fba2bb19e47cf00b8f0514 Mon Sep 17 00:00:00 2001 From: Sofia Stamouli Date: Mon, 31 Jul 2023 17:55:24 +0200 Subject: [PATCH 11/21] Prettier --- tests/modules/nf-core/kmcp/search/test.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/modules/nf-core/kmcp/search/test.yml b/tests/modules/nf-core/kmcp/search/test.yml index 11ae4301b92..7669b72d494 100644 --- a/tests/modules/nf-core/kmcp/search/test.yml +++ b/tests/modules/nf-core/kmcp/search/test.yml @@ -15,4 +15,3 @@ files: - path: output/kmcp/test.gz - path: output/kmcp/versions.yml - From 98aa86fa0ac7fa5185458eab9ed8f1c814143064 Mon Sep 17 00:00:00 2001 From: Sofia Stamouli Date: Mon, 31 Jul 2023 17:57:25 +0200 Subject: [PATCH 12/21] Fix linting --- modules/nf-core/kmcp/search/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/kmcp/search/meta.yml b/modules/nf-core/kmcp/search/meta.yml index d86ae8d172c..5526a179107 100644 --- a/modules/nf-core/kmcp/search/meta.yml +++ b/modules/nf-core/kmcp/search/meta.yml @@ -1,4 +1,4 @@ -name: "kmcp_compute" +name: "kmcp_search" description: Search sequences against database keywords: - metagenomics From 68309ff6e8a0c24237e15532e5664cdbf5a4862b Mon Sep 17 00:00:00 2001 From: Sofia Stamouli Date: Mon, 31 Jul 2023 18:05:16 +0200 Subject: [PATCH 13/21] Update test.yml for kmcp/profile --- tests/modules/nf-core/kmcp/profile/test.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/tests/modules/nf-core/kmcp/profile/test.yml b/tests/modules/nf-core/kmcp/profile/test.yml index 247a42d8dbc..a3fbfb58189 100644 --- a/tests/modules/nf-core/kmcp/profile/test.yml +++ b/tests/modules/nf-core/kmcp/profile/test.yml @@ -4,7 +4,6 @@ - kmcp - kmcp/profile files: - - path: output/kmcp/test.gz - path: output/kmcp/test.profile - path: output/kmcp/versions.yml @@ -14,6 +13,5 @@ - kmcp/profile - kmcp files: - - path: output/kmcp/test.gz - path: output/kmcp/test.profile - path: output/untar/versions.yml From c2bf18d4c87c84af050ab0f7958623ae411eb93a Mon Sep 17 00:00:00 2001 From: Sofia Stamouli Date: Mon, 31 Jul 2023 18:15:46 +0200 Subject: [PATCH 14/21] Update test.yml --- tests/modules/nf-core/kmcp/profile/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/modules/nf-core/kmcp/profile/test.yml b/tests/modules/nf-core/kmcp/profile/test.yml index a3fbfb58189..77f6570ff55 100644 --- a/tests/modules/nf-core/kmcp/profile/test.yml +++ b/tests/modules/nf-core/kmcp/profile/test.yml @@ -14,4 +14,4 @@ - kmcp files: - path: output/kmcp/test.profile - - path: output/untar/versions.yml + - path: output/kmcp/versions.yml From 6e19542370e564069c85817f99e00c7165680c86 Mon Sep 17 00:00:00 2001 From: Sofia Stamouli Date: Mon, 31 Jul 2023 18:34:03 +0200 Subject: [PATCH 15/21] Test without stub --- tests/modules/nf-core/kmcp/profile/test.yml | 8 -------- 1 file changed, 8 deletions(-) diff --git a/tests/modules/nf-core/kmcp/profile/test.yml b/tests/modules/nf-core/kmcp/profile/test.yml index 77f6570ff55..d59e933e0ca 100644 --- a/tests/modules/nf-core/kmcp/profile/test.yml +++ b/tests/modules/nf-core/kmcp/profile/test.yml @@ -7,11 +7,3 @@ - path: output/kmcp/test.profile - path: output/kmcp/versions.yml -- name: kmcp profile test_kmcp_profile stub_run - command: nextflow run ./tests/modules/nf-core/kmcp/profile -entry test_kmcp_profile -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/kmcp/profile/nextflow.config -stub-run - tags: - - kmcp/profile - - kmcp - files: - - path: output/kmcp/test.profile - - path: output/kmcp/versions.yml From d2ea0bcc97910f4fff17e15fb8d207a5f44e02f7 Mon Sep 17 00:00:00 2001 From: Sofia Stamouli Date: Mon, 31 Jul 2023 18:36:07 +0200 Subject: [PATCH 16/21] Prettier --- tests/modules/nf-core/kmcp/profile/test.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/modules/nf-core/kmcp/profile/test.yml b/tests/modules/nf-core/kmcp/profile/test.yml index d59e933e0ca..7834722acf4 100644 --- a/tests/modules/nf-core/kmcp/profile/test.yml +++ b/tests/modules/nf-core/kmcp/profile/test.yml @@ -6,4 +6,3 @@ files: - path: output/kmcp/test.profile - path: output/kmcp/versions.yml - From 3e0cb1246cfe4bbbce3240508a72877d40a07c8e Mon Sep 17 00:00:00 2001 From: Sofia Stamouli Date: Mon, 31 Jul 2023 18:56:54 +0200 Subject: [PATCH 17/21] Add stub to test.yml --- tests/modules/nf-core/kmcp/profile/test.yml | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/tests/modules/nf-core/kmcp/profile/test.yml b/tests/modules/nf-core/kmcp/profile/test.yml index 7834722acf4..6dac88d16e3 100644 --- a/tests/modules/nf-core/kmcp/profile/test.yml +++ b/tests/modules/nf-core/kmcp/profile/test.yml @@ -6,3 +6,12 @@ files: - path: output/kmcp/test.profile - path: output/kmcp/versions.yml + +- name: kmcp profile test_kmcp_profile stub_run + command: nextflow run ./tests/modules/nf-core/kmcp/profile -entry test_kmcp_profile -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/kmcp/profile/nextflow.config -stub-run + tags: + - kmcp + - kmcp/profile + files: + - path: output/kmcp/test.profile + - path: output/kmcp/versions.yml From 612e9cd1e66849e5eb27490f58f2ace3b533a746 Mon Sep 17 00:00:00 2001 From: Sofia Stamouli Date: Tue, 1 Aug 2023 09:22:41 +0200 Subject: [PATCH 18/21] Test gzip in search --- modules/nf-core/kmcp/search/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/kmcp/search/main.nf b/modules/nf-core/kmcp/search/main.nf index b0b5e960406..e31435c3fa6 100644 --- a/modules/nf-core/kmcp/search/main.nf +++ b/modules/nf-core/kmcp/search/main.nf @@ -41,7 +41,7 @@ process KMCP_SEARCH { prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix} - gzip ${prefix} + gzip ${prefix} > ${prefix}.gz cat <<-END_VERSIONS > versions.yml "${task.process}": From 8af0e3f970482e75250fe0d017f21242fc2151ff Mon Sep 17 00:00:00 2001 From: Sofia Stamouli Date: Tue, 1 Aug 2023 09:29:37 +0200 Subject: [PATCH 19/21] Try to fix gzip --- modules/nf-core/kmcp/search/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/kmcp/search/main.nf b/modules/nf-core/kmcp/search/main.nf index e31435c3fa6..2400270e8db 100644 --- a/modules/nf-core/kmcp/search/main.nf +++ b/modules/nf-core/kmcp/search/main.nf @@ -41,7 +41,7 @@ process KMCP_SEARCH { prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix} - gzip ${prefix} > ${prefix}.gz + gzip "${prefix}" cat <<-END_VERSIONS > versions.yml "${task.process}": From c3d2b25572a5e45780166cf7e4f579dcd2d6283d Mon Sep 17 00:00:00 2001 From: Sofia Stamouli Date: Tue, 1 Aug 2023 09:36:49 +0200 Subject: [PATCH 20/21] Try to fix gzip --- modules/nf-core/kmcp/search/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/kmcp/search/main.nf b/modules/nf-core/kmcp/search/main.nf index 2400270e8db..123ad7024ab 100644 --- a/modules/nf-core/kmcp/search/main.nf +++ b/modules/nf-core/kmcp/search/main.nf @@ -41,7 +41,7 @@ process KMCP_SEARCH { prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix} - gzip "${prefix}" + gzip -c "${prefix}" > "${prefix}.gz" cat <<-END_VERSIONS > versions.yml "${task.process}": From 54660a936a88e425d9b9c84a5377efdfea9a56ec Mon Sep 17 00:00:00 2001 From: Sofia Stamouli Date: Tue, 1 Aug 2023 09:48:55 +0200 Subject: [PATCH 21/21] Test gzip --- modules/nf-core/kmcp/search/main.nf | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/modules/nf-core/kmcp/search/main.nf b/modules/nf-core/kmcp/search/main.nf index 123ad7024ab..cb2d68435b7 100644 --- a/modules/nf-core/kmcp/search/main.nf +++ b/modules/nf-core/kmcp/search/main.nf @@ -40,8 +40,7 @@ process KMCP_SEARCH { def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix} - gzip -c "${prefix}" > "${prefix}.gz" + touch ${prefix}.gz cat <<-END_VERSIONS > versions.yml "${task.process}":