From 46652852420ec0be2d64071494f4767aa730590d Mon Sep 17 00:00:00 2001 From: William Eagles Date: Thu, 28 Nov 2024 09:20:25 +0000 Subject: [PATCH 1/7] Remove -M parameter from FastK to resolve segfault issue. --- modules/nf-core/fastk/fastk/main.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/modules/nf-core/fastk/fastk/main.nf b/modules/nf-core/fastk/fastk/main.nf index 67c2dc7a..fe0effd0 100755 --- a/modules/nf-core/fastk/fastk/main.nf +++ b/modules/nf-core/fastk/fastk/main.nf @@ -29,7 +29,6 @@ process FASTK_FASTK { FastK \\ $args \\ -T$task.cpus \\ - -M${task.memory.toGiga()} \\ -N${prefix}_fk \\ $reads From 439b9ecc9ad9334108015b60c697841425ad3b01 Mon Sep 17 00:00:00 2001 From: William Eagles Date: Thu, 28 Nov 2024 11:41:07 +0000 Subject: [PATCH 2/7] Generate module path for fastk --- modules.json | 151 ++++++++++++++----- modules/nf-core/fastk/fastk/fastk-fastk.diff | 11 +- 2 files changed, 121 insertions(+), 41 deletions(-) diff --git a/modules.json b/modules.json index adc156f3..4d6de45a 100755 --- a/modules.json +++ b/modules.json @@ -8,193 +8,268 @@ "bedtools/bamtobed": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/genomecov": { "branch": "master", "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/intersect": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/makewindows": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/map": { "branch": "master", "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/merge": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/sort": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "busco/busco": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/busco/busco/busco-busco.diff" }, "bwamem2/index": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cat/cat": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cooler/cload": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cooler/zoomify": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "custom/dumpsoftwareversions": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "custom/getchromsizes": { "branch": "master", "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/custom/getchromsizes/custom-getchromsizes.diff" }, "fastk/fastk": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ], + "patch": "modules/nf-core/fastk/fastk/fastk-fastk.diff" }, "gnu/sort": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "merquryfk/merquryfk": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "minimap2/align": { "branch": "master", "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/minimap2/align/minimap2-align.diff" }, "minimap2/index": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "miniprot/align": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "miniprot/index": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "mummer": { "branch": "master", "git_sha": "9e51255c4f8ec69fb6ccf68593392835f14fecb8", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/mummer/mummer.diff" }, "paftools/sam2paf": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "pretextmap": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/pretextmap/pretextmap.diff" }, "pretextsnapshot": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/pretextsnapshot/pretextsnapshot.diff" }, "samtools/faidx": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/index": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/markdup": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/merge": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/sort": { "branch": "master", "git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/view": { "branch": "master", "git_sha": "669eb24fd82a9d3cb18ad0e73673ecb26827f683", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "seqtk/cutn": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tabix/bgziptabix": { "branch": "master", "git_sha": "f448e846bdadd80fc8be31fbbc78d9f5b5131a45", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "ucsc/bedgraphtobigwig": { "branch": "master", "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "ucsc/bedtobigbed": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "windowmasker/mkcounts": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "windowmasker/ustat": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] } } }, @@ -203,4 +278,4 @@ } } } -} +} \ No newline at end of file diff --git a/modules/nf-core/fastk/fastk/fastk-fastk.diff b/modules/nf-core/fastk/fastk/fastk-fastk.diff index 56003656..c74973c8 100644 --- a/modules/nf-core/fastk/fastk/fastk-fastk.diff +++ b/modules/nf-core/fastk/fastk/fastk-fastk.diff @@ -1,6 +1,4 @@ Changes in module 'nf-core/fastk/fastk' -'modules/nf-core/fastk/fastk/meta.yml' is unchanged -Changes in 'fastk/fastk/main.nf': --- modules/nf-core/fastk/fastk/main.nf +++ modules/nf-core/fastk/fastk/main.nf @@ -3,7 +3,7 @@ @@ -12,6 +10,13 @@ Changes in 'fastk/fastk/main.nf': input: tuple val(meta), path(reads) +@@ -29,7 +29,6 @@ + FastK \\ + $args \\ + -T$task.cpus \\ +- -M${task.memory.toGiga()} \\ + -N${prefix}_fk \\ + $reads + -'modules/nf-core/fastk/fastk/environment.yml' is unchanged ************************************************************ From e81d671f7943eda05cf5f0d21881349e81a4e278 Mon Sep 17 00:00:00 2001 From: William Eagles Date: Thu, 28 Nov 2024 11:53:04 +0000 Subject: [PATCH 3/7] Prettier --- modules.json | 150 +++++++++++++-------------------------------------- 1 file changed, 38 insertions(+), 112 deletions(-) diff --git a/modules.json b/modules.json index 4d6de45a..4e3d7bc3 100755 --- a/modules.json +++ b/modules.json @@ -8,268 +8,194 @@ "bedtools/bamtobed": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/genomecov": { "branch": "master", "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/intersect": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/makewindows": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/map": { "branch": "master", "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/merge": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/sort": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "busco/busco": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/busco/busco/busco-busco.diff" }, "bwamem2/index": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cat/cat": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cooler/cload": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cooler/zoomify": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "custom/dumpsoftwareversions": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "custom/getchromsizes": { "branch": "master", "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/custom/getchromsizes/custom-getchromsizes.diff" }, "fastk/fastk": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/fastk/fastk/fastk-fastk.diff" }, "gnu/sort": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "merquryfk/merquryfk": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "minimap2/align": { "branch": "master", "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/minimap2/align/minimap2-align.diff" }, "minimap2/index": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "miniprot/align": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "miniprot/index": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "mummer": { "branch": "master", "git_sha": "9e51255c4f8ec69fb6ccf68593392835f14fecb8", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/mummer/mummer.diff" }, "paftools/sam2paf": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "pretextmap": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/pretextmap/pretextmap.diff" }, "pretextsnapshot": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/pretextsnapshot/pretextsnapshot.diff" }, "samtools/faidx": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/index": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/markdup": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/merge": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/sort": { "branch": "master", "git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/view": { "branch": "master", "git_sha": "669eb24fd82a9d3cb18ad0e73673ecb26827f683", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "seqtk/cutn": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tabix/bgziptabix": { "branch": "master", "git_sha": "f448e846bdadd80fc8be31fbbc78d9f5b5131a45", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "ucsc/bedgraphtobigwig": { "branch": "master", "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "ucsc/bedtobigbed": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "windowmasker/mkcounts": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "windowmasker/ustat": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -278,4 +204,4 @@ } } } -} \ No newline at end of file +} From 9b78df145b08271cc7e87b7789018b1e61966a79 Mon Sep 17 00:00:00 2001 From: William Eagles Date: Mon, 2 Dec 2024 16:53:23 +0000 Subject: [PATCH 4/7] Update yahs --- modules.json | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/modules.json b/modules.json index 4e3d7bc3..a429b3b6 100755 --- a/modules.json +++ b/modules.json @@ -196,6 +196,11 @@ "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] + }, + "yahs": { + "branch": "master", + "git_sha": "d3a3d04073af68437f07e0fb9b88aa6172c3f678", + "installed_by": ["modules"] } } }, From e7e36d119b1ef780d643998eaaacf06e45274912 Mon Sep 17 00:00:00 2001 From: William Eagles Date: Wed, 4 Dec 2024 14:20:58 +0000 Subject: [PATCH 5/7] lint fix --- .github/PULL_REQUEST_TEMPLATE.md | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100644 => 100755 .github/PULL_REQUEST_TEMPLATE.md diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md old mode 100644 new mode 100755 From 0bdcf5d953f25084d69f2bd307586654fc6bc46b Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Mon, 9 Dec 2024 16:24:10 +0000 Subject: [PATCH 6/7] Wills MerquryFK update --- docs/usage.md | 5 +- modules.json | 2 +- modules/nf-core/fastk/fastk/environment.yml | 3 +- modules/nf-core/fastk/fastk/fastk-fastk.diff | 8 + modules/nf-core/fastk/fastk/main.nf | 32 ++ modules/nf-core/fastk/fastk/meta.yml | 74 ++-- .../nf-core/fastk/fastk/tests/main.nf.test | 110 ++++++ .../fastk/fastk/tests/main.nf.test.snap | 346 ++++++++++++++++++ .../nf-core/fastk/fastk/tests/nextflow.config | 3 + modules/nf-core/fastk/fastk/tests/tags.yml | 2 + 10 files changed, 553 insertions(+), 32 deletions(-) mode change 100755 => 100644 modules/nf-core/fastk/fastk/main.nf create mode 100644 modules/nf-core/fastk/fastk/tests/main.nf.test create mode 100644 modules/nf-core/fastk/fastk/tests/main.nf.test.snap create mode 100644 modules/nf-core/fastk/fastk/tests/nextflow.config create mode 100644 modules/nf-core/fastk/fastk/tests/tags.yml diff --git a/docs/usage.md b/docs/usage.md index 067a5759..fa94c02f 100755 --- a/docs/usage.md +++ b/docs/usage.md @@ -89,6 +89,8 @@ Now that's all downloaded we need to prep it. At this point it is all still gzip The below code will look through the current folder for files ending with `.fasta.gz` and decompresses it, it will then run our python script, `GA_data_prep.py`. +NOTE: This will soon be superseeded by a rust tools `treeval_utils`, this will replace all of the accessory pythons scripts included in this document. Whilst also adding a program to verify your YAML. + Command: ```bash @@ -234,7 +236,7 @@ If your data isn't already in these formats, then let us know and we'll see how This command iterates through your bam files and converts them to fastq via samtools. -``` +```bash cd { TO FOLDER OF BAM FILES } mkdir fastq for i in *bam @@ -266,6 +268,7 @@ done This simply gzips (compresses) the fasta files. ```bash +cd fasta for i in .fasta; do echo $i gzip $i diff --git a/modules.json b/modules.json index 60db7771..939f0866 100644 --- a/modules.json +++ b/modules.json @@ -79,7 +79,7 @@ }, "fastk/fastk": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"], "patch": "modules/nf-core/fastk/fastk/fastk-fastk.diff" }, diff --git a/modules/nf-core/fastk/fastk/environment.yml b/modules/nf-core/fastk/fastk/environment.yml index 690a3f7a..14207ff6 100644 --- a/modules/nf-core/fastk/fastk/environment.yml +++ b/modules/nf-core/fastk/fastk/environment.yml @@ -1,4 +1,5 @@ -name: fastk_fastk channels: - conda-forge - bioconda +dependencies: + - bioconda::false_flag # False flag to pass nf-core/lint diff --git a/modules/nf-core/fastk/fastk/fastk-fastk.diff b/modules/nf-core/fastk/fastk/fastk-fastk.diff index c74973c8..80906fac 100644 --- a/modules/nf-core/fastk/fastk/fastk-fastk.diff +++ b/modules/nf-core/fastk/fastk/fastk-fastk.diff @@ -18,5 +18,13 @@ Changes in module 'nf-core/fastk/fastk' -N${prefix}_fk \\ $reads +@@ -62,7 +61,6 @@ + "FastK \\ + $args \\ + -T$task.cpus \\ +- -M${task.memory.toGiga()} \\ + -N${prefix}_fk \\ + $reads" + ************************************************************ diff --git a/modules/nf-core/fastk/fastk/main.nf b/modules/nf-core/fastk/fastk/main.nf old mode 100755 new mode 100644 index fe0effd0..256e80de --- a/modules/nf-core/fastk/fastk/main.nf +++ b/modules/nf-core/fastk/fastk/main.nf @@ -32,6 +32,38 @@ process FASTK_FASTK { -N${prefix}_fk \\ $reads + find . -name '*.ktab*' \\ + | xargs chmod a+r + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + fastk: $FASTK_VERSION + END_VERSIONS + """ + + stub: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "FASTK_FASTK module does not support Conda. Please use Docker / Singularity / Podman instead." + } + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def FASTK_VERSION = 'f18a4e6d2207539f7b84461daebc54530a9559b0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + + def touch_ktab = args.contains('-t') ? "touch ${prefix}_fk.ktab .${prefix}_fk.ktab.1" : '' + def touch_prof = args.contains('-p') ? "touch ${prefix}_fk.prof .${prefix}_fk.pidx.1" : '' + """ + touch ${prefix}_fk.hist + $touch_ktab + $touch_prof + + echo \\ + "FastK \\ + $args \\ + -T$task.cpus \\ + -N${prefix}_fk \\ + $reads" + cat <<-END_VERSIONS > versions.yml "${task.process}": fastk: $FASTK_VERSION diff --git a/modules/nf-core/fastk/fastk/meta.yml b/modules/nf-core/fastk/fastk/meta.yml index 7c7f4260..4abc1033 100644 --- a/modules/nf-core/fastk/fastk/meta.yml +++ b/modules/nf-core/fastk/fastk/meta.yml @@ -9,41 +9,57 @@ tools: description: "A fast K-mer counter for high-fidelity shotgun datasets" homepage: "https://github.com/thegenemyers/FASTK" tool_dev_url: "https://github.com/thegenemyers/FASTK" - licence: "https://github.com/thegenemyers/FASTK/blob/master/LICENSE" + licence: ["https://github.com/thegenemyers/FASTK/blob/master/LICENSE"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - hist: - type: file - description: Histogram of k-mers - pattern: "*.hist" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hist": + type: file + description: Histogram of k-mers + pattern: "*.hist" - ktab: - type: file - description: A sorted table of all canonical k‑mers along with their counts. - pattern: "*.ktab" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - '*.ktab*", hidden: true': + type: file + description: A sorted table of all canonical k‑mers along with their counts. + pattern: "*.ktab" - prof: - type: file - description: A k‑mer count profile of each sequence in the input data set. - pattern: "*.prof" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - '*.{prof,pidx}*", hidden: true': + type: file + description: A k‑mer count profile of each sequence in the input data set. + pattern: "*.prof" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: - "@mahesh-panchal" + - "@gallvp" diff --git a/modules/nf-core/fastk/fastk/tests/main.nf.test b/modules/nf-core/fastk/fastk/tests/main.nf.test new file mode 100644 index 00000000..856c36a8 --- /dev/null +++ b/modules/nf-core/fastk/fastk/tests/main.nf.test @@ -0,0 +1,110 @@ +nextflow_process { + + name "Test Process FASTK_FASTK" + script "../main.nf" + config './nextflow.config' + process "FASTK_FASTK" + + tag "modules" + tag "modules_nfcore" + tag "fastk" + tag "fastk/fastk" + + test("test_fastk_fastk_single_end") { + when { + process { + """ + input[0] = [ + [ id:'test' , single_end: true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("test_fastk_fastk_paired_end") { + + when { + process { + """ + input[0] = [ + [ id:'test' , single_end: false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("test_fastk_fastk_single_end_stub") { + + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test' , single_end: true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("test_fastk_fastk_paired_end_stub") { + + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test' , single_end: false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/fastk/fastk/tests/main.nf.test.snap b/modules/nf-core/fastk/fastk/tests/main.nf.test.snap new file mode 100644 index 00000000..1e3fc4da --- /dev/null +++ b/modules/nf-core/fastk/fastk/tests/main.nf.test.snap @@ -0,0 +1,346 @@ +{ + "test_fastk_fastk_single_end_stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test_fk.hist:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + [ + ".test_fk.ktab.1:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_fk.ktab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": true + }, + [ + ".test_fk.pidx.1:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_fk.prof:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "3": [ + 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b/modules/nf-core/fastk/fastk/tests/tags.yml @@ -0,0 +1,2 @@ +fastk/fastk: + - "modules/nf-core/fastk/fastk/**" From c55ea9b2af561c0efdc4f6666835553827517813 Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Mon, 9 Dec 2024 16:28:56 +0000 Subject: [PATCH 7/7] Revert modules.json to previous PR --- modules.json | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/modules.json b/modules.json index 939f0866..5d6662aa 100644 --- a/modules.json +++ b/modules.json @@ -12,7 +12,7 @@ }, "bedtools/genomecov": { "branch": "master", - "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83", + "git_sha": "bfa8975eefb8df3e480a44ac9e594f23f52b2963", "installed_by": ["modules"] }, "bedtools/intersect": { @@ -27,7 +27,7 @@ }, "bedtools/map": { "branch": "master", - "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "bedtools/merge": { @@ -58,12 +58,12 @@ }, "cooler/cload": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "cooler/zoomify": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "custom/dumpsoftwareversions": { @@ -96,7 +96,7 @@ }, "minimap2/align": { "branch": "master", - "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"], "patch": "modules/nf-core/minimap2/align/minimap2-align.diff" }, @@ -117,9 +117,8 @@ }, "mummer": { "branch": "master", - "git_sha": "9e51255c4f8ec69fb6ccf68593392835f14fecb8", - "installed_by": ["modules"], - "patch": "modules/nf-core/mummer/mummer.diff" + "git_sha": "a15872dde4c4affaac2dfee6c3c65fadab4719bd", + "installed_by": ["modules"] }, "paftools/sam2paf": { "branch": "master",