From 0b56869fdfe955c357486810e5bf1d2c834da833 Mon Sep 17 00:00:00 2001 From: Olga Botvinnik Date: Wed, 25 Jun 2025 09:40:51 -0700 Subject: [PATCH 1/2] Remove nf-core/interproscan module --- modules/nf-core/interproscan/environment.yml | 7 - modules/nf-core/interproscan/main.nf | 66 ------ modules/nf-core/interproscan/meta.yml | 82 ------- .../nf-core/interproscan/tests/main.nf.test | 100 --------- .../interproscan/tests/main.nf.test.snap | 207 ------------------ .../interproscan/tests/nextflow.config | 5 - modules/nf-core/interproscan/tests/tags.yml | 2 - 7 files changed, 469 deletions(-) delete mode 100644 modules/nf-core/interproscan/environment.yml delete mode 100644 modules/nf-core/interproscan/main.nf delete mode 100644 modules/nf-core/interproscan/meta.yml delete mode 100644 modules/nf-core/interproscan/tests/main.nf.test delete mode 100644 modules/nf-core/interproscan/tests/main.nf.test.snap delete mode 100644 modules/nf-core/interproscan/tests/nextflow.config delete mode 100644 modules/nf-core/interproscan/tests/tags.yml diff --git a/modules/nf-core/interproscan/environment.yml b/modules/nf-core/interproscan/environment.yml deleted file mode 100644 index 8e82f00..0000000 --- a/modules/nf-core/interproscan/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -channels: - - conda-forge - - bioconda -dependencies: - - bioconda::interproscan=5.59_91.0 diff --git a/modules/nf-core/interproscan/main.nf b/modules/nf-core/interproscan/main.nf deleted file mode 100644 index add9b03..0000000 --- a/modules/nf-core/interproscan/main.nf +++ /dev/null @@ -1,66 +0,0 @@ -process INTERPROSCAN { - tag "$meta.id" - label 'process_medium' - label 'process_long' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/interproscan:5.59_91.0--hec16e2b_1' : - 'biocontainers/interproscan:5.59_91.0--hec16e2b_1' }" - - input: - tuple val(meta), path(fasta) - path(interproscan_database, stageAs: 'data') - - output: - tuple val(meta), path('*.tsv') , optional: true, emit: tsv - tuple val(meta), path('*.xml') , optional: true, emit: xml - tuple val(meta), path('*.gff3'), optional: true, emit: gff3 - tuple val(meta), path('*.json'), optional: true, emit: json - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def is_compressed = fasta.name.endsWith(".gz") - def fasta_name = fasta.name.replace(".gz", "") - """ - if [ -d 'data' ]; then - # Find interproscan.properties to link data/ from work directory - INTERPROSCAN_DIR="\$( dirname "\$( dirname "\$( which interproscan.sh )" )" )" - INTERPROSCAN_PROPERTIES="\$( find "\$INTERPROSCAN_DIR/share" -name "interproscan.properties" )" - cp "\$INTERPROSCAN_PROPERTIES" . - sed -i "/^bin\\.directory=/ s|.*|bin.directory=\$INTERPROSCAN_DIR/bin|" interproscan.properties - export INTERPROSCAN_CONF=interproscan.properties - fi # else use sample DB included with conda ( testing only! ) - - if ${is_compressed} ; then - gzip -c -d ${fasta} > ${fasta_name} - fi - - interproscan.sh \\ - --cpu ${task.cpus} \\ - --input ${fasta_name} \\ - ${args} \\ - --output-file-base ${prefix} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - interproscan: \$( interproscan.sh --version | sed '1!d; s/.*version //' ) - END_VERSIONS - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.{tsv,xml,json,gff3} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - interproscan: \$( interproscan.sh --version | sed '1!d; s/.*version //' ) - END_VERSIONS - """ -} diff --git a/modules/nf-core/interproscan/meta.yml b/modules/nf-core/interproscan/meta.yml deleted file mode 100644 index 0bb10f7..0000000 --- a/modules/nf-core/interproscan/meta.yml +++ /dev/null @@ -1,82 +0,0 @@ -name: "interproscan" -description: Produces protein annotations and predictions from an amino acids FASTA - file -keywords: - - annotation - - fasta - - protein - - dna - - interproscan -tools: - - "interproscan": - description: "InterPro integrates together predictive information about proteins - function from a number of partner resources" - homepage: "https://www.ebi.ac.uk/interpro/search/sequence/" - documentation: "https://interproscan-docs.readthedocs.io" - tool_dev_url: "https://github.com/ebi-pf-team/interproscan" - doi: "10.1093/bioinformatics/btu031" - licence: ["GPL v3"] - identifier: "" -input: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input fasta file containing the amino acid or dna query sequences - pattern: "*.{fa,fasta,fa.gz,fasta.gz}" - - - interproscan_database: - type: directory - description: Path to the interproscan database (untarred - http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/${version_major}-${version_minor}/interproscan-${version_major}-${version_minor}-64-bit.tar.gz) -output: - - tsv: - - meta: - type: file - description: Tab separated file containing with detailed hits - pattern: "*.{tsv}" - - "*.tsv": - type: file - description: Tab separated file containing with detailed hits - pattern: "*.{tsv}" - - xml: - - meta: - type: file - description: XML file containing with detailed hits - pattern: "*.{xml}" - - "*.xml": - type: file - description: XML file containing with detailed hits - pattern: "*.{xml}" - - gff3: - - meta: - type: file - description: GFF3 file containing with detailed hits - pattern: "*.{gff3}" - - "*.gff3": - type: file - description: GFF3 file containing with detailed hits - pattern: "*.{gff3}" - - json: - - meta: - type: file - description: JSON file containing with detailed hits - pattern: "*.{json}" - - "*.json": - type: file - description: JSON file containing with detailed hits - pattern: "*.{json}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@toniher" - - "@mahesh-panchal" -maintainers: - - "@toniher" - - "@vagkaratzas" - - "@mahesh-panchal" diff --git a/modules/nf-core/interproscan/tests/main.nf.test b/modules/nf-core/interproscan/tests/main.nf.test deleted file mode 100644 index 1fe4625..0000000 --- a/modules/nf-core/interproscan/tests/main.nf.test +++ /dev/null @@ -1,100 +0,0 @@ -nextflow_process { - - name "Test Process INTERPROSCAN" - script "../main.nf" - process "INTERPROSCAN" - config "./nextflow.config" - tag "modules" - tag "modules_nfcore" - tag "interproscan" - - // Note: Regular tests have been commented out because Interproscan has a harded coded a requirement of 10G memory, - // and so will therefore not run on the nf-core test runners without being killed. - - // test("sarscov2 - proteome_fasta") { - - // when { - // process { - // """ - // input[0] = [ - // [ id:'test' ], - // file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true) - // ] - // input[1] = [] - // """ - // } - // } - - // then { - // assertAll( - // { assert process.success }, - // { assert snapshot( - // path(process.out.tsv[0][1]).readLines()[0] - // .contains("ENSSASP00005000004.1 4c35f09aac2f7be4f3cffd30c6aecac8 1273 Coils Coil Coil 1176 1203 - T"), - // process.out.xml, - // process.out.json, - // path(process.out.gff3[0][1]).readLines()[0..4,6..-1], - // process.out.versions, - // ).match() - // } - // ) - // } - - // } - - // test("sarscov2 - proteome_fasta_gz") { - - // when { - // process { - // """ - // input[0] = [ - // [ id:'test' ], - // file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta.gz', checkIfExists: true) - // ] - // input[1] = [] - // """ - // } - // } - - // then { - // assertAll( - // { assert process.success }, - // { assert snapshot( - // path(process.out.tsv[0][1]).readLines()[0] - // .contains("ENSSASP00005000004.1 4c35f09aac2f7be4f3cffd30c6aecac8 1273 Coils Coil Coil 1176 1203 - T"), - // process.out.xml, - // process.out.json, - // path(process.out.gff3[0][1]).readLines()[0..4,6..-1], - // process.out.versions, - // ).match() - // } - // ) - // } - - // } - - test("sarscov2 - proteome_fasta_gz - stub") { - - options '-stub' - - when { - process { - """ - input[0] = [ - [ id:'test' ], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta.gz', checkIfExists: true) - ] - input[1] = [] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - - } -} diff --git a/modules/nf-core/interproscan/tests/main.nf.test.snap b/modules/nf-core/interproscan/tests/main.nf.test.snap deleted file mode 100644 index 0529dfe..0000000 --- a/modules/nf-core/interproscan/tests/main.nf.test.snap +++ /dev/null @@ -1,207 +0,0 @@ -{ - "sarscov2 - proteome_fasta_gz - stub": { - "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - { - "id": "test" - }, - "test.xml:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - [ - { - "id": "test" - }, - "test.gff3:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "3": [ - [ - { - "id": "test" - }, - "test.json:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "4": [ - "versions.yml:md5,8bd8c66c2f1a7854faa29781761642c2" - ], - "gff3": [ - [ - { - "id": "test" - }, - "test.gff3:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "json": [ - [ - { - "id": "test" - }, - "test.json:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "tsv": [ - [ - { - "id": "test" - }, - "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,8bd8c66c2f1a7854faa29781761642c2" - ], - "xml": [ - [ - { - "id": "test" - }, - "test.xml:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.1" - }, - "timestamp": "2024-05-27T12:51:27.943051636" - }, - "sarscov2 - proteome_fasta_gz": { - "content": [ - true, - [ - [ - { - "id": "test" - }, - "test.xml:md5,7a211c1a4761e2b9b8700e6e9abbb15f" - ] - ], - [ - [ - { - "id": "test" - }, - "test.json:md5,b05cffc28b7bfeb3dabe43c2927b2024" - ] - ], - [ - "##gff-version 3", - "##feature-ontology http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269", - "##interproscan-version 5.59-91.0", - "##sequence-region ENSSASP00005000004.1 1 1273", - "ENSSASP00005000004.1\t.\tpolypeptide\t1\t1273\t.\t+\t.\tID=ENSSASP00005000004.1;md5=4c35f09aac2f7be4f3cffd30c6aecac8", - "##FASTA", - ">ENSSASP00005000004.1", - "MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFS", - "NVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIV", - "NNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLE", - "GKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT", - "LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETK", - "CTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISN", - "CVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIAD", - "YNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC", - "NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVN", - "FNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITP", - "GTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSY", - "ECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI", - "SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQE", - "VFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDC", - "LGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAM", - "QMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALN", - "TLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA", - "SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPA", - "ICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP", - "LQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL", - "QELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDD", - "SEPVLKGVKLHYT", - ">match$1_1176_1203", - "VVNIQKEIDRLNEVAKNLNESLIDLQEL" - ], - [ - "versions.yml:md5,8bd8c66c2f1a7854faa29781761642c2" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.1" - }, - "timestamp": "2024-05-27T12:51:14.476645388" - }, - "sarscov2 - proteome_fasta": { - "content": [ - true, - [ - [ - { - "id": "test" - }, - "test.xml:md5,7a211c1a4761e2b9b8700e6e9abbb15f" - ] - ], - [ - [ - { - "id": "test" - }, - "test.json:md5,b05cffc28b7bfeb3dabe43c2927b2024" - ] - ], - [ - "##gff-version 3", - "##feature-ontology http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269", - "##interproscan-version 5.59-91.0", - "##sequence-region ENSSASP00005000004.1 1 1273", - "ENSSASP00005000004.1\t.\tpolypeptide\t1\t1273\t.\t+\t.\tID=ENSSASP00005000004.1;md5=4c35f09aac2f7be4f3cffd30c6aecac8", - "##FASTA", - ">ENSSASP00005000004.1", - "MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFS", - "NVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIV", - "NNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLE", - "GKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT", - "LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETK", - "CTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISN", - "CVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIAD", - "YNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC", - "NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVN", - "FNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITP", - "GTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSY", - "ECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI", - "SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQE", - "VFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDC", - "LGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAM", - "QMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALN", - "TLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA", - "SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPA", - "ICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP", - "LQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL", - "QELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDD", - "SEPVLKGVKLHYT", - ">match$1_1176_1203", - "VVNIQKEIDRLNEVAKNLNESLIDLQEL" - ], - [ - "versions.yml:md5,8bd8c66c2f1a7854faa29781761642c2" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.1" - }, - "timestamp": "2024-05-27T12:50:27.562653728" - } -} \ No newline at end of file diff --git a/modules/nf-core/interproscan/tests/nextflow.config b/modules/nf-core/interproscan/tests/nextflow.config deleted file mode 100644 index 2043e2c..0000000 --- a/modules/nf-core/interproscan/tests/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - withName: INTERPROSCAN { - ext.args = '-appl Coils' - } -} diff --git a/modules/nf-core/interproscan/tests/tags.yml b/modules/nf-core/interproscan/tests/tags.yml deleted file mode 100644 index ddb90f8..0000000 --- a/modules/nf-core/interproscan/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -interproscan: - - modules/nf-core/interproscan/** From 7e39138aac7e17fd7aab83a9ec1ee9095ba5df3f Mon Sep 17 00:00:00 2001 From: Olga Botvinnik Date: Wed, 25 Jun 2025 10:00:05 -0700 Subject: [PATCH 2/2] Remove interproscan from modules.json --- modules.json | 5 ----- 1 file changed, 5 deletions(-) diff --git a/modules.json b/modules.json index 459aef4..48b44eb 100644 --- a/modules.json +++ b/modules.json @@ -5,11 +5,6 @@ "https://github.com/nf-core/modules.git": { "modules": { "nf-core": { - "interproscan": { - "branch": "master", - "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", - "installed_by": ["modules"] - }, "mmseqs/search": { "branch": "master", "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",