From 44f238e45d7181daaf73f65829efa8606801f322 Mon Sep 17 00:00:00 2001 From: Tyler Chafin Date: Tue, 10 Dec 2024 16:35:32 +0000 Subject: [PATCH 1/2] removed merquryfk --- CHANGELOG.md | 5 +- modules.json | 64 ++- modules/nf-core/merquryfk/merquryfk/main.nf | 80 --- .../merquryfk/merquryfk-merquryfk.diff | 16 - modules/nf-core/merquryfk/merquryfk/meta.yml | 217 --------- .../merquryfk/merquryfk/tests/main.nf.test | 170 ------- .../merquryfk/tests/main.nf.test.snap | 454 ------------------ .../merquryfk/merquryfk/tests/nextflow.config | 8 - .../merquryfk/tests/nextflow.pdf.config | 9 - .../merquryfk/tests/nextflow.png.config | 9 - .../merquryfk/tests/nextflow.trio.config | 9 - .../merquryfk/merquryfk/tests/tags.yml | 2 - subworkflows/local/genome_statistics.nf | 26 +- 13 files changed, 61 insertions(+), 1008 deletions(-) delete mode 100644 modules/nf-core/merquryfk/merquryfk/main.nf delete mode 100644 modules/nf-core/merquryfk/merquryfk/merquryfk-merquryfk.diff delete mode 100644 modules/nf-core/merquryfk/merquryfk/meta.yml delete mode 100644 modules/nf-core/merquryfk/merquryfk/tests/main.nf.test delete mode 100644 modules/nf-core/merquryfk/merquryfk/tests/main.nf.test.snap delete mode 100644 modules/nf-core/merquryfk/merquryfk/tests/nextflow.config delete mode 100644 modules/nf-core/merquryfk/merquryfk/tests/nextflow.pdf.config delete mode 100644 modules/nf-core/merquryfk/merquryfk/tests/nextflow.png.config delete mode 100644 modules/nf-core/merquryfk/merquryfk/tests/nextflow.trio.config delete mode 100644 modules/nf-core/merquryfk/merquryfk/tests/tags.yml diff --git a/CHANGELOG.md b/CHANGELOG.md index 9a313b1b..345c3250 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,13 +3,14 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## [[2.1.0](https://github.com/sanger-tol/genomenote/releases/tag/2.1.0)] - Pembroke Welsh Corgi [2024-12-05] +## [[2.1.0](https://github.com/sanger-tol/genomenote/releases/tag/2.1.0)] - Pembroke Welsh Corgi [2024-12-11] ### Enhancements & fixes - New annotation_statistics subworkfow which runs BUSCO in protein mode and generates some basic statistics on the the annotated gene set if provided with a GFF3 file of gene annotations using the `--annotation_set` option. - The genome_metadata subworkflow now queries Ensembl's GraphQL API to determine if Ensembl has released gene annotation for the assembly being processed. - Module updates and remove Anaconda channels +- Removed merquryfk completeness metric ### Parameters @@ -31,7 +32,7 @@ Note, since the pipeline is using Nextflow DSL2, each process will be run with i | `cooler` | 0.8.11 | 0.9.2 | | `fastk` | 427104ea91c78c3b8b8b49f1a7d6bbeaa869ba1c | 666652151335353eef2fcd58880bcef5bc2928e1 | | `gffread` | | 0.12.7 | -| `merquryfk` | d00d98157618f4e8d1a9190026b19b471055b22e | 666652151335353eef2fcd58880bcef5bc2928e1 | +| `merquryfk` | d00d98157618f4e8d1a9190026b19b471055b22e | | | `multiqc` | 1.14 | 1.25.1 | | `samtools` | 1.17 | 1.21 | diff --git a/modules.json b/modules.json index bc77dc22..ff107640 100644 --- a/modules.json +++ b/modules.json @@ -8,83 +8,105 @@ "agat/spstatistics": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "agat/sqstatbasic": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/bamtobed": { "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" }, "cooler/cload": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cooler/dump": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cooler/zoomify": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "custom/dumpsoftwareversions": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "fastk/fastk": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/fastk/fastk/fastk-fastk.diff" }, "gffread": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gnu/sort": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "gunzip": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] - }, - "merquryfk/merquryfk": { - "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"], - "patch": "modules/nf-core/merquryfk/merquryfk/merquryfk-merquryfk.diff" + "installed_by": [ + "modules" + ] }, "multiqc": { "branch": "master", "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/view": { "branch": "master", "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] } } } } } -} +} \ No newline at end of file diff --git a/modules/nf-core/merquryfk/merquryfk/main.nf b/modules/nf-core/merquryfk/merquryfk/main.nf deleted file mode 100644 index 2a5ab221..00000000 --- a/modules/nf-core/merquryfk/merquryfk/main.nf +++ /dev/null @@ -1,80 +0,0 @@ -process MERQURYFK_MERQURYFK { - tag "$meta.id" - label 'process_medium' - - // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. - container 'ghcr.io/nbisweden/fastk_genescopefk_merquryfk:1.2' - - input: - tuple val(meta), path(fastk_hist),path(fastk_ktab),path(assembly),path(haplotigs) - path matktab //optional - path patktab //optional - - output: - tuple val(meta), path("${prefix}.completeness.stats") , emit: stats - tuple val(meta), path("${prefix}.*_only.bed") , emit: bed - tuple val(meta), path("${prefix}.*.qv") , emit: assembly_qv - tuple val(meta), path("${prefix}.*.spectra-cn.fl.{png,pdf}") , emit: spectra_cn_fl, optional: true - tuple val(meta), path("${prefix}.*.spectra-cn.ln.{png,pdf}") , emit: spectra_cn_ln, optional: true - tuple val(meta), path("${prefix}.*.spectra-cn.st.{png,pdf}") , emit: spectra_cn_st, optional: true - tuple val(meta), path("${prefix}.qv") , emit: qv - tuple val(meta), path("${prefix}.spectra-asm.fl.{png,pdf}") , emit: spectra_asm_fl, optional: true - tuple val(meta), path("${prefix}.spectra-asm.ln.{png,pdf}") , emit: spectra_asm_ln, optional: true - tuple val(meta), path("${prefix}.spectra-asm.st.{png,pdf}") , emit: spectra_asm_st, optional: true - tuple val(meta), path("${prefix}.phased_block.bed") , emit: phased_block_bed, optional: true - tuple val(meta), path("${prefix}.phased_block.stats") , emit: phased_block_stats, optional: true - tuple val(meta), path("${prefix}.continuity.N.{pdf,png}") , emit: continuity_N, optional: true - tuple val(meta), path("${prefix}.block.N.{pdf,png}") , emit: block_N, optional: true - tuple val(meta), path("${prefix}.block.blob.{pdf,png}") , emit: block_blob, optional: true - tuple val(meta), path("${prefix}.hapmers.blob.{pdf,png}") , emit: hapmers_blob, optional: true - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "MERQURYFK_MERQURYFK module does not support Conda. Please use Docker / Singularity / Podman instead." - } - def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${meta.id}" - def mat_ktab = matktab ? "${matktab.find{ it.toString().endsWith(".ktab") }}" : '' - def pat_ktab = patktab ? "${patktab.find{ it.toString().endsWith(".ktab") }}" : '' - def FASTK_VERSION = '666652151335353eef2fcd58880bcef5bc2928e1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. - def MERQURY_VERSION = '666652151335353eef2fcd58880bcef5bc2928e1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. - """ - MerquryFK \\ - $args \\ - -T$task.cpus \\ - ${fastk_ktab.find{ it.toString().endsWith(".ktab") }} \\ - ${mat_ktab} \\ - ${pat_ktab} \\ - $assembly \\ - $haplotigs \\ - $prefix - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastk: $FASTK_VERSION - merquryfk: $MERQURY_VERSION - r: \$( R --version | sed '1!d; s/.*version //; s/ .*//' ) - END_VERSIONS - """ - stub: - prefix = task.ext.prefix ?: "${meta.id}" - def FASTK_VERSION = 'f18a4e6d2207539f7b84461daebc54530a9559b0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. - def MERQURY_VERSION = '8ae344092df5dcaf83cfb7f90f662597a9b1fc61' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. - """ - touch ${prefix}.completeness.stats - touch ${prefix}.qv - touch ${prefix}._.qv - touch ${prefix}._only.bed - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastk: $FASTK_VERSION - merquryfk: $MERQURY_VERSION - r: \$( R --version | sed '1!d; s/.*version //; s/ .*//' ) - END_VERSIONS - """ -} diff --git a/modules/nf-core/merquryfk/merquryfk/merquryfk-merquryfk.diff b/modules/nf-core/merquryfk/merquryfk/merquryfk-merquryfk.diff deleted file mode 100644 index b0ecbe5d..00000000 --- a/modules/nf-core/merquryfk/merquryfk/merquryfk-merquryfk.diff +++ /dev/null @@ -1,16 +0,0 @@ -Changes in module 'nf-core/merquryfk/merquryfk' ---- modules/nf-core/merquryfk/merquryfk/main.nf -+++ modules/nf-core/merquryfk/merquryfk/main.nf -@@ -41,8 +41,8 @@ - prefix = task.ext.prefix ?: "${meta.id}" - def mat_ktab = matktab ? "${matktab.find{ it.toString().endsWith(".ktab") }}" : '' - def pat_ktab = patktab ? "${patktab.find{ it.toString().endsWith(".ktab") }}" : '' -- def FASTK_VERSION = 'f18a4e6d2207539f7b84461daebc54530a9559b0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. -- def MERQURY_VERSION = '8ae344092df5dcaf83cfb7f90f662597a9b1fc61' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. -+ def FASTK_VERSION = '666652151335353eef2fcd58880bcef5bc2928e1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. -+ def MERQURY_VERSION = '666652151335353eef2fcd58880bcef5bc2928e1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. - """ - MerquryFK \\ - $args \\ - -************************************************************ diff --git a/modules/nf-core/merquryfk/merquryfk/meta.yml b/modules/nf-core/merquryfk/merquryfk/meta.yml deleted file mode 100644 index 82bfbec4..00000000 --- a/modules/nf-core/merquryfk/merquryfk/meta.yml +++ /dev/null @@ -1,217 +0,0 @@ -name: "merquryfk_merquryfk" -description: FastK based version of Merqury -keywords: - - Merqury - - reference-free - - assembly evaluation -tools: - - "merquryfk": - description: "FastK based version of Merqury" - homepage: "https://github.com/thegenemyers/MERQURY.FK" - tool_dev_url: "https://github.com/thegenemyers/MERQURY.FK" - licence: ["https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE"] - identifier: "" -input: - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastk_hist: - type: file - description: A histogram files from the program FastK - pattern: "*.hist" - - fastk_ktab: - type: file - description: Histogram ktab files from the program FastK (option -t) - pattern: "*.ktab*" - - assembly: - type: file - description: Genome (primary) assembly files (fasta format) - pattern: ".fasta" - - haplotigs: - type: file - description: Assembly haplotigs (fasta format) - pattern: ".fasta" - - - matktab: - type: file - description: trio maternal histogram ktab files from the program FastK (option - -t) - pattern: "*.ktab*" - - - patktab: - type: file - description: trio paternal histogram ktab files from the program FastK (option - -t) - pattern: "*.ktab*" -output: - - stats: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ${prefix}.completeness.stats: - type: file - description: Assembly statistics file - pattern: "*.completeness.stats" - - bed: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ${prefix}.*_only.bed: - type: file - description: Assembly only kmer positions not supported by reads in bed format - pattern: "*_only.bed" - - assembly_qv: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ${prefix}.*.qv: - type: file - description: "error and qv table for each scaffold of the assembly" - pattern: "*.qv" - - spectra_cn_fl: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ${prefix}.*.spectra-cn.fl.{png,pdf}: - type: file - description: "Unstacked copy number spectra filled plot in PNG or PDF format" - pattern: "*.spectra-cn.fl.{png,pdf}" - - spectra_cn_ln: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ${prefix}.*.spectra-cn.ln.{png,pdf}: - type: file - description: "Unstacked copy number spectra line plot in PNG or PDF format" - pattern: "*.spectra-cn.ln.{png,pdf}" - - spectra_cn_st: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ${prefix}.*.spectra-cn.st.{png,pdf}: - type: file - description: "Stacked copy number spectra line plot in PNG or PDF format" - pattern: "*.spectra-cn.st.{png,pdf}" - - qv: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ${prefix}.qv: - type: file - description: "error and qv of each assembly as a whole" - pattern: "*.qv" - - spectra_asm_fl: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ${prefix}.spectra-asm.fl.{png,pdf}: - type: file - description: "Unstacked assembly spectra filled plot in PNG or PDF format" - pattern: "*.spectra-asm.fl.{png,pdf}" - - spectra_asm_ln: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ${prefix}.spectra-asm.ln.{png,pdf}: - type: file - description: "Unstacked assembly spectra line plot in PNG or PDF format" - pattern: "*.spectra-asm.ln.{png,pdf}" - - spectra_asm_st: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ${prefix}.spectra-asm.st.{png,pdf}: - type: file - description: "Stacked assembly spectra line plot in PNG or PDF format" - pattern: "*.spectra-asm.st.{png,pdf}" - - phased_block_bed: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ${prefix}.phased_block.bed: - type: file - description: Assembly kmer positions seperated by block in bed format - pattern: "*.phased.block.bed" - - phased_block_stats: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ${prefix}.phased_block.stats: - type: file - description: phased assembly statistics file - pattern: "*.phased.block.stats" - - continuity_N: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ${prefix}.continuity.N.{pdf,png}: - type: file - description: "Stacked assembly N continuity plot in PNG or PDF format" - pattern: "*.continuity.N.{png,pdf}" - - block_N: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ${prefix}.block.N.{pdf,png}: - type: file - description: "Stacked assembly N continuity by block plot in PNG or PDF format" - pattern: "*.block.N.{png,pdf}" - - block_blob: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ${prefix}.block.blob.{pdf,png}: - type: file - description: "Stacked assembly block plot in PNG or PDF format" - pattern: "*.block.blob.{png,pdf}" - - hapmers_blob: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ${prefix}.hapmers.blob.{pdf,png}: - type: file - description: "Stacked assembly hapmers block plot in PNG or PDF format" - pattern: "*.hapmers.blob.{png,pdf}" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@mahesh-panchal" - - "@yumisims" -maintainers: - - "@mahesh-panchal" - - "@yumisims" diff --git a/modules/nf-core/merquryfk/merquryfk/tests/main.nf.test b/modules/nf-core/merquryfk/merquryfk/tests/main.nf.test deleted file mode 100644 index c46843c6..00000000 --- a/modules/nf-core/merquryfk/merquryfk/tests/main.nf.test +++ /dev/null @@ -1,170 +0,0 @@ -nextflow_process { - - name "Test Process MERQURYFK" - script "../main.nf" - process "MERQURYFK_MERQURYFK" - - tag "modules" - tag "modules_nfcore" - tag "merquryfk" - tag "merquryfk/merquryfk" - tag "fastk" - tag "fastk/fastk" - - setup { - run("FASTK_FASTK") { - script "../../../fastk/fastk" - process { - """ - input[0] = [ - [ id:'test', single_end:false ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz', checkIfExists: true) - ] - """ - } - } - run("FASTK_FASTK", alias: "FASTK_MAT") { - script "../../../fastk/fastk" - process { - """ - input[0] = [ - [ id:'test', single_end:false ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - ] - """ - } - } - - run("FASTK_FASTK", alias: "FASTK_PAT") { - script "../../../fastk/fastk" - process { - """ - input[0] = [ - [ id:'test', single_end:false ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz', checkIfExists: true), - ] - """ - } - } - } - - test("homo_sapiens - Illumina - png") { - config "./nextflow.png.config" - when { - process { - """ - assembly = [ - [ id:'test', single_end:true ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) - ] - - haplotigs = [ - [ id:'test', single_end:true ], [] - ] - input[0] = FASTK_FASTK.out.hist.join(FASTK_FASTK.out.ktab).join(Channel.from(assembly)).join(Channel.from(haplotigs)) - input[1] = [] - input[2] = [] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - - } - - test("homo_sapiens - Illumina - pdf") { - config "./nextflow.pdf.config" - when { - process { - """ - assembly = [ - [ id:'test', single_end:true ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) - ] - - haplotigs = [ - [ id:'test', single_end:true ], [] - ] - input[0] = FASTK_FASTK.out.hist.join(FASTK_FASTK.out.ktab).join(Channel.from(assembly)).join(Channel.from(haplotigs)) - input[1] = [] - input[2] = [] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - - } - - test("homo_sapiens - Illumina - trio") { - config "./nextflow.trio.config" - when { - process { - """ - assembly = [ - [ id:'test', single_end:true ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) - ] - - haplotigs = [ - [ id:'test', single_end:true ], [] - ] - input[0] = FASTK_FASTK.out.hist.join(FASTK_FASTK.out.ktab).join(Channel.from(assembly)).join(Channel.from(haplotigs)) - input[1] = FASTK_MAT.out.ktab - input[2] = FASTK_PAT.out.ktab - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - - } - - test("homo_sapiens - Illumina - stub") { - options "-stub" - config "./nextflow.pdf.config" - when { - process { - """ - assembly = [ - [ id:'test', single_end:true ], - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) - ] - - haplotigs = [ - [ id:'test', single_end:true ], [] - ] - input[0] = FASTK_FASTK.out.hist.join(FASTK_FASTK.out.ktab).join(Channel.from(assembly)).join(Channel.from(haplotigs)) - input[1] = [] - input[2] = [] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - - } - - - -} \ No newline at end of file diff --git a/modules/nf-core/merquryfk/merquryfk/tests/main.nf.test.snap b/modules/nf-core/merquryfk/merquryfk/tests/main.nf.test.snap deleted file mode 100644 index f7ce47f0..00000000 --- a/modules/nf-core/merquryfk/merquryfk/tests/main.nf.test.snap +++ /dev/null @@ -1,454 +0,0 @@ -{ - "homo_sapiens - Illumina - stub": { - "content": [ - { - "0": [ - - ], - "1": [ - - ], - "10": [ - - ], - "11": [ - - ], - "12": [ - - ], - "13": [ - - ], - "14": [ - - ], - "15": [ - - ], - "16": [ - - ], - "2": [ - - ], - "3": [ - - ], - "4": [ - - ], - "5": [ - - ], - "6": [ - - ], - "7": [ - - ], - "8": [ - - ], - "9": [ - - ], - "assembly_qv": [ - - ], - "bed": [ - - ], - "block_N": [ - - ], - "block_blob": [ - - ], - "continuity_N": [ - - ], - "hapmers_blob": [ - - ], - "phased_block_bed": [ - - ], - "phased_block_stats": [ - - ], - "qv": [ - - ], - "spectra_asm_fl": [ - - ], - "spectra_asm_ln": [ - - ], - "spectra_asm_st": [ - - ], - "spectra_cn_fl": [ - - ], - "spectra_cn_ln": [ - - ], - "spectra_cn_st": [ - - ], - "stats": [ - - ], - "versions": [ - - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-08-15T15:22:52.240373868" - }, - "homo_sapiens - Illumina - pdf": { - "content": [ - { - "0": [ - - ], - "1": [ - - ], - "10": [ - - ], - "11": [ - - ], - "12": [ - - ], - "13": [ - - ], - "14": [ - - ], - "15": [ - - ], - "16": [ - - ], - "2": [ - - ], - "3": [ - - ], - "4": [ - - ], - "5": [ - - ], - "6": [ - - ], - "7": [ - - ], - "8": [ - - ], - "9": [ - - ], - "assembly_qv": [ - - ], - "bed": [ - - ], - "block_N": [ - - ], - "block_blob": [ - - ], - "continuity_N": [ - - ], - "hapmers_blob": [ - - ], - "phased_block_bed": [ - - ], - "phased_block_stats": [ - - ], - "qv": [ - - ], - "spectra_asm_fl": [ - - ], - "spectra_asm_ln": [ - - ], - "spectra_asm_st": [ - - ], - "spectra_cn_fl": [ - - ], - "spectra_cn_ln": [ - - ], - "spectra_cn_st": [ - - ], - "stats": [ - - ], - "versions": [ - - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-08-15T15:22:19.530675341" - }, - "homo_sapiens - Illumina - png": { - "content": [ - { - "0": [ - - ], - "1": [ - - ], - "10": [ - - ], - "11": [ - - ], - "12": [ - - ], - "13": [ - - ], - "14": [ - - ], - "15": [ - - ], - "16": [ - - ], - "2": [ - - ], - "3": [ - - ], - "4": [ - - ], - "5": [ - - ], - "6": [ - - ], - "7": [ - - ], - "8": [ - - ], - "9": [ - - ], - "assembly_qv": [ - - ], - "bed": [ - - ], - "block_N": [ - - ], - "block_blob": [ - - ], - "continuity_N": [ - - ], - "hapmers_blob": [ - - ], - "phased_block_bed": [ - - ], - "phased_block_stats": [ - - ], - "qv": [ - - ], - "spectra_asm_fl": [ - - ], - "spectra_asm_ln": [ - - ], - "spectra_asm_st": [ - - ], - "spectra_cn_fl": [ - - ], - "spectra_cn_ln": [ - - ], - "spectra_cn_st": [ - - ], - "stats": [ - - ], - "versions": [ - - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-08-15T15:21:57.682723412" - }, - "homo_sapiens - Illumina - trio": { - "content": [ - { - "0": [ - - ], - "1": [ - - ], - "10": [ - - ], - "11": [ - - ], - "12": [ - - ], - "13": [ - - ], - "14": [ - - ], - "15": [ - - ], - "16": [ - - ], - "2": [ - - ], - "3": [ - - ], - "4": [ - - ], - "5": [ - - ], - "6": [ - - ], - "7": [ - - ], - "8": [ - - ], - "9": [ - - ], - "assembly_qv": [ - - ], - "bed": [ - - ], - "block_N": [ - - ], - "block_blob": [ - - ], - "continuity_N": [ - - ], - "hapmers_blob": [ - - ], - "phased_block_bed": [ - - ], - "phased_block_stats": [ - - ], - "qv": [ - - ], - "spectra_asm_fl": [ - - ], - "spectra_asm_ln": [ - - ], - "spectra_asm_st": [ - - ], - "spectra_cn_fl": [ - - ], - "spectra_cn_ln": [ - - ], - "spectra_cn_st": [ - - ], - "stats": [ - - ], - "versions": [ - - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-08-15T15:22:40.060937299" - } -} \ No newline at end of file diff --git a/modules/nf-core/merquryfk/merquryfk/tests/nextflow.config b/modules/nf-core/merquryfk/merquryfk/tests/nextflow.config deleted file mode 100644 index ba1eebc9..00000000 --- a/modules/nf-core/merquryfk/merquryfk/tests/nextflow.config +++ /dev/null @@ -1,8 +0,0 @@ -process { - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: 'FASTK_.*' { - ext.args = '-t' - publishDir = [ enabled: false ] - } -} diff --git a/modules/nf-core/merquryfk/merquryfk/tests/nextflow.pdf.config b/modules/nf-core/merquryfk/merquryfk/tests/nextflow.pdf.config deleted file mode 100644 index 52beeaa3..00000000 --- a/modules/nf-core/merquryfk/merquryfk/tests/nextflow.pdf.config +++ /dev/null @@ -1,9 +0,0 @@ -process { - withName: 'FASTK_.*' { - ext.args = '-t' - publishDir = [ enabled: false ] - } - withName: 'MERQURYFK_MERQURYFK' { - ext.args = '-lfs -pdf' - } -} diff --git a/modules/nf-core/merquryfk/merquryfk/tests/nextflow.png.config b/modules/nf-core/merquryfk/merquryfk/tests/nextflow.png.config deleted file mode 100644 index 47c3d63e..00000000 --- a/modules/nf-core/merquryfk/merquryfk/tests/nextflow.png.config +++ /dev/null @@ -1,9 +0,0 @@ -process { - withName: 'FASTK_.*' { - ext.args = '-t' - publishDir = [ enabled: false ] - } - withName: 'MERQURYFK_MERQURYFK' { - ext.args = '-lfs' - } -} diff --git a/modules/nf-core/merquryfk/merquryfk/tests/nextflow.trio.config b/modules/nf-core/merquryfk/merquryfk/tests/nextflow.trio.config deleted file mode 100644 index 47c3d63e..00000000 --- a/modules/nf-core/merquryfk/merquryfk/tests/nextflow.trio.config +++ /dev/null @@ -1,9 +0,0 @@ -process { - withName: 'FASTK_.*' { - ext.args = '-t' - publishDir = [ enabled: false ] - } - withName: 'MERQURYFK_MERQURYFK' { - ext.args = '-lfs' - } -} diff --git a/modules/nf-core/merquryfk/merquryfk/tests/tags.yml b/modules/nf-core/merquryfk/merquryfk/tests/tags.yml deleted file mode 100644 index 7dcac99b..00000000 --- a/modules/nf-core/merquryfk/merquryfk/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -merquryfk/merquryfk: - - "modules/nf-core/merquryfk/merquryfk/**" diff --git a/subworkflows/local/genome_statistics.nf b/subworkflows/local/genome_statistics.nf index e8807f96..758e5920 100644 --- a/subworkflows/local/genome_statistics.nf +++ b/subworkflows/local/genome_statistics.nf @@ -8,9 +8,10 @@ include { NCBI_GET_ODB } from '../../modules/lo include { BUSCO_BUSCO as BUSCO } from '../../modules/nf-core/busco/busco/main' include { RESTRUCTUREBUSCODIR } from '../../modules/local/restructurebuscodir' include { FASTK_FASTK } from '../../modules/nf-core/fastk/fastk/main' -include { MERQURYFK_MERQURYFK } from '../../modules/nf-core/merquryfk/merquryfk/main' include { CREATETABLE } from '../../modules/local/createtable' +// This is only temporarily removed so I'm leaving it here for now +//include { MERQURYFK_MERQURYFK } from '../../modules/nf-core/merquryfk/merquryfk/main' workflow GENOME_STATISTICS { take: @@ -103,9 +104,10 @@ workflow GENOME_STATISTICS { | set { ch_merq } - // MerquryFK - MERQURYFK_MERQURYFK ( ch_merq, [], [] ) - ch_versions = ch_versions.mix ( MERQURYFK_MERQURYFK.out.versions.first() ) + // This is only temporarily removed so I'm leaving it here for now + // // MerquryFK + // MERQURYFK_MERQURYFK ( ch_merq, [], [] ) + // ch_versions = ch_versions.mix ( MERQURYFK_MERQURYFK.out.versions.first() ) // Combined table @@ -117,12 +119,13 @@ workflow GENOME_STATISTICS { | ifEmpty ( [ [], [] ] ) | set { ch_busco } - MERQURYFK_MERQURYFK.out.qv - | join ( MERQURYFK_MERQURYFK.out.stats ) - | map { meta, qv, comp -> [ meta + [ id: "merq" ], qv, comp ] } - | groupTuple () - | ifEmpty ( [ [], [], [] ] ) - | set { ch_merqury } + // This is only temporarily removed so I'm leaving it here for now + // MERQURYFK_MERQURYFK.out.qv + // | join ( MERQURYFK_MERQURYFK.out.stats ) + // | map { meta, qv, comp -> [ meta + [ id: "merq" ], qv, comp ] } + // | groupTuple () + // | ifEmpty ( [ [], [], [] ] ) + // | set { ch_merqury } flagstat // Queue channel of tuple(meta, file) @@ -135,7 +138,8 @@ workflow GENOME_STATISTICS { // Now channel of tuple(list(meta), list(file)) | set { ch_flagstat } - CREATETABLE ( ch_summary, ch_busco, ch_merqury, ch_flagstat ) + //CREATETABLE ( ch_summary, ch_busco, ch_merqury, ch_flagstat ) + CREATETABLE ( ch_summary, ch_busco, [[], [], []], ch_flagstat ) ch_versions = ch_versions.mix ( CREATETABLE.out.versions.first() ) From 8add69e7f8794012e36cbb6a63978c7df784e409 Mon Sep 17 00:00:00 2001 From: Tyler Chafin Date: Tue, 10 Dec 2024 18:55:13 +0000 Subject: [PATCH 2/2] prettier linting --- modules.json | 58 ++++++++++++++-------------------------------------- 1 file changed, 15 insertions(+), 43 deletions(-) diff --git a/modules.json b/modules.json index ff107640..05680e71 100644 --- a/modules.json +++ b/modules.json @@ -8,105 +8,77 @@ "agat/spstatistics": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "agat/sqstatbasic": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/bamtobed": { "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" }, "cooler/cload": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cooler/dump": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cooler/zoomify": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "custom/dumpsoftwareversions": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "fastk/fastk": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/fastk/fastk/fastk-fastk.diff" }, "gffread": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gnu/sort": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "gunzip": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "multiqc": { "branch": "master", "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/view": { "branch": "master", "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } } } } -} \ No newline at end of file +}