From 65145ce68e567d364c7ac1b617a61d216ba1c4ef Mon Sep 17 00:00:00 2001 From: Tyler Chafin Date: Tue, 24 Sep 2024 10:43:10 +0100 Subject: [PATCH 01/17] patch 1.3.1 --- conf/base.config | 5 + conf/modules.config | 6 +- modules.json | 10 +- .../bbmap/filterbyname/environment.yml | 5 + modules/nf-core/bbmap/filterbyname/main.nf | 71 ++++++ modules/nf-core/bbmap/filterbyname/meta.yml | 70 ++++++ .../bbmap/filterbyname/tests/main.nf.test | 218 ++++++++++++++++++ .../filterbyname/tests/main.nf.test.snap | 145 ++++++++++++ .../nf-core/bbmap/filterbyname/tests/tags.yml | 2 + modules/nf-core/seqtk/subseq/environment.yml | 7 - modules/nf-core/seqtk/subseq/main.nf | 56 ----- modules/nf-core/seqtk/subseq/meta.yml | 40 ---- .../nf-core/seqtk/subseq/tests/main.nf.test | 59 ----- .../seqtk/subseq/tests/main.nf.test.snap | 60 ----- .../seqtk/subseq/tests/standard.config | 5 - modules/nf-core/seqtk/subseq/tests/tags.yml | 2 - subworkflows/local/align_short.nf | 6 +- subworkflows/local/filter_pacbio.nf | 12 +- 18 files changed, 535 insertions(+), 244 deletions(-) create mode 100644 modules/nf-core/bbmap/filterbyname/environment.yml create mode 100644 modules/nf-core/bbmap/filterbyname/main.nf create mode 100644 modules/nf-core/bbmap/filterbyname/meta.yml create mode 100644 modules/nf-core/bbmap/filterbyname/tests/main.nf.test create mode 100644 modules/nf-core/bbmap/filterbyname/tests/main.nf.test.snap create mode 100644 modules/nf-core/bbmap/filterbyname/tests/tags.yml delete mode 100644 modules/nf-core/seqtk/subseq/environment.yml delete mode 100644 modules/nf-core/seqtk/subseq/main.nf delete mode 100644 modules/nf-core/seqtk/subseq/meta.yml delete mode 100644 modules/nf-core/seqtk/subseq/tests/main.nf.test delete mode 100644 modules/nf-core/seqtk/subseq/tests/main.nf.test.snap delete mode 100644 modules/nf-core/seqtk/subseq/tests/standard.config delete mode 100644 modules/nf-core/seqtk/subseq/tests/tags.yml diff --git a/conf/base.config b/conf/base.config index ca753f3..3827aae 100644 --- a/conf/base.config +++ b/conf/base.config @@ -41,6 +41,11 @@ process { memory = { check_max( ((meta.datatype == "pacbio_clr" || meta.datatype == "ont") ? 2.GB : 1.GB) * task.attempt, 'memory' ) } } + // minimum 1GB memory + withName: 'BBMAP_FILTERBYNAME' { + memory = { check_max( 1.GB, 'memory' ) } + } + withName: 'SAMTOOLS_COLLATETOFASTA' { cpus = { log_increase_cpus(4, 2*task.attempt, 1, 2) } memory = { check_max( 1.GB * Math.ceil( meta.read_count / 1000000 ) * task.attempt, 'memory' ) } diff --git a/conf/modules.config b/conf/modules.config index a2d4464..d05fe4b 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -15,12 +15,16 @@ process { ext.args = '-F 0x200 -nt' } + withName: BBMAP_FILTERBYNAME { + ext.args = 'include=f' + } + withName: '.*:.*:ALIGN_HIC:BWAMEM2_MEM' { ext.args = { "-5SPCp -R ${meta.read_group}" } } withName: '.*:.*:ALIGN_ILLUMINA:BWAMEM2_MEM' { - ext.args = { "-R ${meta.read_group}" } + ext.args = { "-p -R ${meta.read_group}" } } withName: SAMTOOLS_MERGE { diff --git a/modules.json b/modules.json index b7bb93d..522bb30 100644 --- a/modules.json +++ b/modules.json @@ -5,6 +5,11 @@ "https://github.com/nf-core/modules.git": { "modules": { "nf-core": { + "bbmap/filterbyname": { + "branch": "master", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "installed_by": ["modules"] + }, "blast/blastn": { "branch": "master", "git_sha": "583edaf97c9373a20df05a3b7be5a6677f9cd719", @@ -81,11 +86,6 @@ "git_sha": "03fbf6c89e551bd8d77f3b751fb5c955f75b34c5", "installed_by": ["modules"] }, - "seqtk/subseq": { - "branch": "master", - "git_sha": "730f3aee80d5f8d0b5fc532202ac59361414d006", - "installed_by": ["modules"] - }, "untar": { "branch": "master", "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", diff --git a/modules/nf-core/bbmap/filterbyname/environment.yml b/modules/nf-core/bbmap/filterbyname/environment.yml new file mode 100644 index 0000000..dfd8936 --- /dev/null +++ b/modules/nf-core/bbmap/filterbyname/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::bbmap=39.01 diff --git a/modules/nf-core/bbmap/filterbyname/main.nf b/modules/nf-core/bbmap/filterbyname/main.nf new file mode 100644 index 0000000..7267908 --- /dev/null +++ b/modules/nf-core/bbmap/filterbyname/main.nf @@ -0,0 +1,71 @@ +process BBMAP_FILTERBYNAME { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bbmap:39.01--h5c4e2a8_0': + 'biocontainers/bbmap:39.01--h5c4e2a8_0' }" + + input: + tuple val(meta), path(reads) + val(names_to_filter) + val(output_format) + val(interleaved_output) + + output: + tuple val(meta), path("*.${output_format}"), emit: reads + tuple val(meta), path('*.log') , emit: log + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def input = meta.single_end ? "in=${reads}" : "in=${reads[0]} in2=${reads[1]}" + def output = (meta.single_end || interleaved_output) ? + "out=${prefix}.${output_format}" : + "out1=${prefix}_1.${output_format} out2=${prefix}_2.${output_format}" + def names_command = names_to_filter ? "names=${names_to_filter}": "" + + def avail_mem = 3 + if (!task.memory) { + log.info '[filterbyname] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' + } else { + avail_mem = task.memory.giga + } + + """ + filterbyname.sh \\ + -Xmx${avail_mem}g \\ + $input \\ + $output \\ + $names_command \\ + $args \\ + | tee ${prefix}.log + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bbmap: \$(bbversion.sh | grep -v "Duplicate cpuset") + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def filtered = (meta.single_end || interleaved_output) ? + "echo '' | gzip > ${prefix}.${output_format}" : + "echo '' | gzip >${prefix}_1.${output_format} ; echo '' | gzip >${prefix}_2.${output_format}" + + """ + $filtered + touch ${prefix}.log + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bbmap: \$(bbversion.sh | grep -v "Duplicate cpuset") + END_VERSIONS + """ + +} diff --git a/modules/nf-core/bbmap/filterbyname/meta.yml b/modules/nf-core/bbmap/filterbyname/meta.yml new file mode 100644 index 0000000..b7b8641 --- /dev/null +++ b/modules/nf-core/bbmap/filterbyname/meta.yml @@ -0,0 +1,70 @@ +name: bbmap_filterbyname +description: Filter out sequences by sequence header name(s) +keywords: + - fastq + - fasta + - filter +tools: + - bbmap: + description: BBMap is a short read aligner, as well as various other bioinformatic + tools. + homepage: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/clumpify-guide/ + documentation: https://www.biostars.org/p/225338/ + licence: ["UC-LBL license (see package)"] + identifier: biotools:bbmap + +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. + - - names_to_filter: + type: string + description: | + String containing names of reads to filter out of the fastq files. + - - output_format: + type: string + description: | + String with the format of the output file, e.g. fastq.gz, fasta, fasta.bz2 + - - interleaved_output: + type: boolean + description: | + Whether to produce an interleaved fastq output file +output: + - reads: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${output_format}": + type: file + description: The trimmed/modified fastq reads + pattern: "*${output_format}" + - log: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: filterbyname.sh log file + pattern: "*.filterbyname.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@tokarevvasily" + - "@sppearce" + +maintainers: + - "@sppearce" diff --git a/modules/nf-core/bbmap/filterbyname/tests/main.nf.test b/modules/nf-core/bbmap/filterbyname/tests/main.nf.test new file mode 100644 index 0000000..17c7ea5 --- /dev/null +++ b/modules/nf-core/bbmap/filterbyname/tests/main.nf.test @@ -0,0 +1,218 @@ +nextflow_process { + + name "Test Process BBMAP_FILTERBYNAME" + script "../main.nf" + process "BBMAP_FILTERBYNAME" + + tag "modules" + tag "modules_nfcore" + tag "bbmap" + tag "bbmap/filterbyname" + + test("paired end fastq.bz2") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + 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) + ] + input[1] = "" + input[2] = "fastq.bz2" + input[3] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match() } + ) + } + + } + + test("paired end fastq.bz2 - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + 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) + ] + input[1] = "" + input[2] = "fastq.bz2" + input[3] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("single end fasta") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + input[1] = "" + input[2] = "fasta" + input[3] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match() } + ) + } + + } + + test("single end fasta - stub") { + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + input[1] = "" + input[2] = "fasta" + input[3] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match() } + ) + } + + } + + test("single end fastq.gz filter") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + input[1] = "ERR5069949.2151832,ERR5069949.576388,ERR5069949.501486" + input[2] = "fasta" + input[3] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match() } + ) + } + + } + + test("single end fastq.gz - stub") { + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + input[1] = "ERR5069949.2151832,ERR5069949.576388,ERR5069949.501486" + input[2] = "fastq.gz" + input[3] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match() } + ) + } + + } + + test("paired end fastq.gz filter interleaved") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + 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) + ] + input[1] = "ERR5069949.2151832,ERR5069949.576388,ERR5069949.501486" + input[2] = "fastq.gz" + input[3] = true + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match() } + ) + } + + } + + test("paired end fastq.gz filter interleaved - stub") { + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + 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) + ] + input[1] = "ERR5069949.2151832,ERR5069949.576388,ERR5069949.501486" + input[2] = "fastq.gz" + input[3] = true + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match() } + ) + } + + } + +} diff --git a/modules/nf-core/bbmap/filterbyname/tests/main.nf.test.snap b/modules/nf-core/bbmap/filterbyname/tests/main.nf.test.snap new file mode 100644 index 0000000..e06845a --- /dev/null +++ b/modules/nf-core/bbmap/filterbyname/tests/main.nf.test.snap @@ -0,0 +1,145 @@ +{ + "single end fasta": { + "content": [ + [ + "versions.yml:md5,aaa9e9267785f8680ba0cab91423c06d" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-13T12:10:54.50002639" + }, + "paired end fastq.bz2": { + "content": [ + [ + "versions.yml:md5,aaa9e9267785f8680ba0cab91423c06d" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-13T12:10:31.368676493" + }, + "paired end fastq.bz2 - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.fastq.bz2:md5,1a60c330fb42841e8dcf3cd507a70bfc", + "test_2.fastq.bz2:md5,1a60c330fb42841e8dcf3cd507a70bfc" + ] + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,aaa9e9267785f8680ba0cab91423c06d" + ], + "log": [ + [ + { + "id": "test", + "single_end": false + }, + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "reads": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.fastq.bz2:md5,1a60c330fb42841e8dcf3cd507a70bfc", + "test_2.fastq.bz2:md5,1a60c330fb42841e8dcf3cd507a70bfc" + ] + ] + ], + "versions": [ + "versions.yml:md5,aaa9e9267785f8680ba0cab91423c06d" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-13T12:10:42.854788269" + }, + "single end fastq.gz filter": { + "content": [ + [ + "versions.yml:md5,aaa9e9267785f8680ba0cab91423c06d" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-13T12:11:24.280900344" + }, + "single end fastq.gz - stub": { + "content": [ + [ + "versions.yml:md5,aaa9e9267785f8680ba0cab91423c06d" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-13T12:11:43.274477064" + }, + "paired end fastq.gz filter interleaved - stub": { + "content": [ + [ + "versions.yml:md5,aaa9e9267785f8680ba0cab91423c06d" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-13T12:12:05.324554457" + }, + "single end fasta - stub": { + "content": [ + [ + "versions.yml:md5,aaa9e9267785f8680ba0cab91423c06d" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-13T12:11:13.161430777" + }, + "paired end fastq.gz filter interleaved": { + "content": [ + [ + "versions.yml:md5,aaa9e9267785f8680ba0cab91423c06d" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-13T12:11:54.599067108" + } +} diff --git a/modules/nf-core/bbmap/filterbyname/tests/tags.yml b/modules/nf-core/bbmap/filterbyname/tests/tags.yml new file mode 100644 index 0000000..707f910 --- /dev/null +++ b/modules/nf-core/bbmap/filterbyname/tests/tags.yml @@ -0,0 +1,2 @@ +bbmap/filterbyname: + - "modules/nf-core/bbmap/filterbyname/**" diff --git a/modules/nf-core/seqtk/subseq/environment.yml b/modules/nf-core/seqtk/subseq/environment.yml deleted file mode 100644 index 7abe364..0000000 --- a/modules/nf-core/seqtk/subseq/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ -name: seqtk_subseq -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - bioconda::seqtk=1.4 diff --git a/modules/nf-core/seqtk/subseq/main.nf b/modules/nf-core/seqtk/subseq/main.nf deleted file mode 100644 index d5caebc..0000000 --- a/modules/nf-core/seqtk/subseq/main.nf +++ /dev/null @@ -1,56 +0,0 @@ -process SEQTK_SUBSEQ { - tag "$sequences" - label 'process_single' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/seqtk:1.4--he4a0461_1' : - 'biocontainers/seqtk:1.4--he4a0461_1' }" - - input: - tuple val(meta), path(sequences) - path filter_list - - output: - tuple val(meta), path("*.gz"), emit: sequences - path "versions.yml", emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def ext = "fa" - if ("$sequences" ==~ /.+\.fq|.+\.fq.gz|.+\.fastq|.+\.fastq.gz/) { - ext = "fq" - } - """ - seqtk \\ - subseq \\ - $args \\ - $sequences \\ - $filter_list | \\ - gzip --no-name > ${sequences}${prefix}.${ext}.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//') - END_VERSIONS - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - def ext = "fa" - if ("$sequences" ==~ /.+\.fq|.+\.fq.gz|.+\.fastq|.+\.fastq.gz/) { - ext = "fq" - } - """ - echo "" | gzip > ${sequences}${prefix}.${ext}.gz - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//') - END_VERSIONS - """ -} diff --git a/modules/nf-core/seqtk/subseq/meta.yml b/modules/nf-core/seqtk/subseq/meta.yml deleted file mode 100644 index de4a841..0000000 --- a/modules/nf-core/seqtk/subseq/meta.yml +++ /dev/null @@ -1,40 +0,0 @@ -name: seqtk_subseq -description: Select only sequences that match the filtering condition -keywords: - - filtering - - selection - - fastx -tools: - - seqtk: - description: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format - homepage: https://github.com/lh3/seqtk - documentation: https://docs.csc.fi/apps/seqtk/ - tool_dev_url: https://github.com/lh3/seqtk - licence: ["MIT"] -input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - sequences: - type: file - description: FASTQ/FASTA file - pattern: "*.{fq,fq.gz,fa,fa.gz}" - - filter_list: - type: file - description: BED file or a text file with a list of sequence names - pattern: "*.{bed,lst}" -output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - sequences: - type: file - description: FASTQ/FASTA file - pattern: "*.{fq.gz,fa.gz}" -authors: - - "@sidorov-si" -maintainers: - - "@sidorov-si" diff --git a/modules/nf-core/seqtk/subseq/tests/main.nf.test b/modules/nf-core/seqtk/subseq/tests/main.nf.test deleted file mode 100644 index fa8fad6..0000000 --- a/modules/nf-core/seqtk/subseq/tests/main.nf.test +++ /dev/null @@ -1,59 +0,0 @@ -nextflow_process { - - name "Test Process SEQTK_SUBSEQ" - script "modules/nf-core/seqtk/subseq/main.nf" - process "SEQTK_SUBSEQ" - config "./standard.config" - - tag "modules" - tag "modules_nfcore" - tag "seqtk" - tag "seqtk/subseq" - - test("sarscov2_subseq_fa") { - - when { - process { - """ - input[0] = [ - [ id:'test' ], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed.gz', checkIfExists: true) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - - } - - test("sarscov2_subseq_fa_stub") { - options "-stub" - when { - process { - """ - input[0] = [ - [ id:'test' ], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - ] - input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed.gz', checkIfExists: true) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - - } - -} diff --git a/modules/nf-core/seqtk/subseq/tests/main.nf.test.snap b/modules/nf-core/seqtk/subseq/tests/main.nf.test.snap deleted file mode 100644 index 75b3793..0000000 --- a/modules/nf-core/seqtk/subseq/tests/main.nf.test.snap +++ /dev/null @@ -1,60 +0,0 @@ -{ - "sarscov2_subseq_fa": { - "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "genome.fasta.filtered.fa.gz:md5,31c95c4d686526cf002f6119bc55b2b2" - ] - ], - "1": [ - "versions.yml:md5,cd7682f4da748ef6d083c4a4656cc1e2" - ], - "sequences": [ - [ - { - "id": "test" - }, - "genome.fasta.filtered.fa.gz:md5,31c95c4d686526cf002f6119bc55b2b2" - ] - ], - "versions": [ - "versions.yml:md5,cd7682f4da748ef6d083c4a4656cc1e2" - ] - } - ], - "timestamp": "2024-02-22T15:56:36.155954" - }, - "sarscov2_subseq_fa_stub": { - "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "genome.fasta.filtered.fa.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "1": [ - "versions.yml:md5,cd7682f4da748ef6d083c4a4656cc1e2" - ], - "sequences": [ - [ - { - "id": "test" - }, - "genome.fasta.filtered.fa.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] - ], - "versions": [ - "versions.yml:md5,cd7682f4da748ef6d083c4a4656cc1e2" - ] - } - ], - "timestamp": "2024-02-22T15:56:44.222329" - } -} \ No newline at end of file diff --git a/modules/nf-core/seqtk/subseq/tests/standard.config b/modules/nf-core/seqtk/subseq/tests/standard.config deleted file mode 100644 index e8d7dc3..0000000 --- a/modules/nf-core/seqtk/subseq/tests/standard.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - withName: SEQTK_SUBSEQ { - ext.prefix = { ".filtered" } - } -} \ No newline at end of file diff --git a/modules/nf-core/seqtk/subseq/tests/tags.yml b/modules/nf-core/seqtk/subseq/tests/tags.yml deleted file mode 100644 index 74056ba..0000000 --- a/modules/nf-core/seqtk/subseq/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -seqtk/subseq: - - "modules/nf-core/seqtk/subseq/**" diff --git a/subworkflows/local/align_short.nf b/subworkflows/local/align_short.nf index e74b480..f189135 100644 --- a/subworkflows/local/align_short.nf +++ b/subworkflows/local/align_short.nf @@ -29,10 +29,10 @@ workflow ALIGN_SHORT { // Convert from CRAM to FASTQ only if CRAM files were provided as input - SAMTOOLS_FASTQ ( ch_reads.cram, false ) + SAMTOOLS_FASTQ ( ch_reads.cram, true ) ch_versions = ch_versions.mix ( SAMTOOLS_FASTQ.out.versions.first() ) - - + + SAMTOOLS_FASTQ.out.fastq | mix ( ch_reads.fastq ) | set { ch_reads_fastq } diff --git a/subworkflows/local/filter_pacbio.nf b/subworkflows/local/filter_pacbio.nf index acb21fa..5edb338 100644 --- a/subworkflows/local/filter_pacbio.nf +++ b/subworkflows/local/filter_pacbio.nf @@ -9,7 +9,7 @@ include { BLAST_BLASTN } from '../../modules/nf-core/blast/ include { PACBIO_FILTER } from '../../modules/local/pacbio_filter' include { SAMTOOLS_FILTERTOFASTQ } from '../../modules/local/samtools_filtertofastq' include { SEQKIT_FQ2FA } from '../../modules/nf-core/seqkit/fq2fa' -include { SEQTK_SUBSEQ } from '../../modules/nf-core/seqtk/subseq' +include { BBMAP_FILTERBYNAME } from '../../modules/nf-core/bbmap/filterbyname' workflow FILTER_PACBIO { @@ -67,7 +67,7 @@ workflow FILTER_PACBIO { ch_versions = ch_versions.mix ( PACBIO_FILTER.out.versions.first() ) - // Filter the BAM files and convert to FASTQ + // Filter the input BAM and output as interleaved FASTA SAMTOOLS_CONVERT.out.bam | join ( SAMTOOLS_CONVERT.out.csi ) | join ( PACBIO_FILTER.out.list ) @@ -81,7 +81,7 @@ workflow FILTER_PACBIO { ch_versions = ch_versions.mix ( SAMTOOLS_FILTERTOFASTQ.out.versions.first() ) - // Filter inputs provided as FASTQ + // Filter inputs provided as FASTQ and output as interleaved FASTQ ch_reads.fastq | join(PACBIO_FILTER.out.list) | multiMap { meta, fastq, list -> \ @@ -90,12 +90,12 @@ workflow FILTER_PACBIO { } | set { ch_reads_fastq } - SEQTK_SUBSEQ ( ch_reads_fastq.fastqs, ch_reads_fastq.lists ) - ch_versions = ch_versions.mix ( SEQTK_SUBSEQ.out.versions.first() ) + BBMAP_FILTERBYNAME ( ch_reads_fastq.fastqs, ch_reads_fastq.lists , "fastq", true) + ch_versions = ch_versions.mix ( BBMAP_FILTERBYNAME.out.versions.first() ) // Merge filtered outputs as ch_output_fastq - SEQTK_SUBSEQ.out.sequences + BBMAP_FILTERBYNAME.out.reads | concat ( SAMTOOLS_FILTERTOFASTQ.out.fastq ) | set { ch_filtered_fastq } From 35b26b72561e76fd41223af0571c84d4c91c56cd Mon Sep 17 00:00:00 2001 From: Tyler Chafin Date: Tue, 24 Sep 2024 10:49:01 +0100 Subject: [PATCH 02/17] pass interleaved fastq after cram conversion --- subworkflows/local/align_short.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/align_short.nf b/subworkflows/local/align_short.nf index f189135..3fdf330 100644 --- a/subworkflows/local/align_short.nf +++ b/subworkflows/local/align_short.nf @@ -33,7 +33,7 @@ workflow ALIGN_SHORT { ch_versions = ch_versions.mix ( SAMTOOLS_FASTQ.out.versions.first() ) - SAMTOOLS_FASTQ.out.fastq + SAMTOOLS_FASTQ.out.interleaved_fastq | mix ( ch_reads.fastq ) | set { ch_reads_fastq } From 414ac2a808b5a803bd5fc44ab4197e2f7e920534 Mon Sep 17 00:00:00 2001 From: Tyler Chafin Date: Tue, 24 Sep 2024 10:50:30 +0100 Subject: [PATCH 03/17] Update align_short.nf --- subworkflows/local/align_short.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/align_short.nf b/subworkflows/local/align_short.nf index 3fdf330..6b58e4e 100644 --- a/subworkflows/local/align_short.nf +++ b/subworkflows/local/align_short.nf @@ -33,7 +33,7 @@ workflow ALIGN_SHORT { ch_versions = ch_versions.mix ( SAMTOOLS_FASTQ.out.versions.first() ) - SAMTOOLS_FASTQ.out.interleaved_fastq + SAMTOOLS_FASTQ.out.interleaved | mix ( ch_reads.fastq ) | set { ch_reads_fastq } From 0c96567c22e6fb54420bf9152e21d6378507a72a Mon Sep 17 00:00:00 2001 From: Tyler Chafin Date: Tue, 24 Sep 2024 10:57:02 +0100 Subject: [PATCH 04/17] Update CHANGELOG.md --- CHANGELOG.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ca9294f..3854131 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,13 @@ 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). +## [[1.3.1](https://github.com/sanger-tol/readmapping/releases/tag/1.3.0)] - Antipodean Opaleye - [2024-09-24] + +### Enhancements & fixes + +- Fixed bug in handling CRAM HiC inputs introduced in 1.1.0 +- Fixed bug in handling PacBio FASTQ inputs introduced in 1.3.0 + ## [[1.3.0](https://github.com/sanger-tol/readmapping/releases/tag/1.3.0)] - Antipodean Opaleye - [2024-08-23] ### Enhancements & fixes From 5b4f685f21d24ad33bb350bc895100e629b7a4ee Mon Sep 17 00:00:00 2001 From: Tyler Chafin Date: Tue, 24 Sep 2024 10:57:34 +0100 Subject: [PATCH 05/17] Update nextflow.config --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 437ff82..35f7911 100644 --- a/nextflow.config +++ b/nextflow.config @@ -232,7 +232,7 @@ manifest { description = 'Pipeline to map reads generated using different sequencing technologies against a genome assembly.' mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '1.3.0' + version = '1.3.1' doi = '10.5281/zenodo.6563577' } From e4d43981299aa024bbbfaf4923c2d3174a03bd27 Mon Sep 17 00:00:00 2001 From: Tyler Chafin Date: Tue, 24 Sep 2024 11:20:12 +0100 Subject: [PATCH 06/17] Update LICENSE --- LICENSE | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/LICENSE b/LICENSE index e238724..a9bcd4d 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) @priyanka-surana +Copyright (c) 2022-2024 Genome Research Ltd. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal From 86a38626c2854c1253cde00c973413e17c4d63fa Mon Sep 17 00:00:00 2001 From: Tyler Chafin Date: Tue, 24 Sep 2024 11:29:24 +0100 Subject: [PATCH 07/17] Update download_pipeline.yml --- .github/workflows/download_pipeline.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index bd9f7bf..36fbc9d 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -10,7 +10,7 @@ on: testbranch: description: "The specific branch you wish to utilize for the test execution of nf-core download." required: true - default: "dev" + default: "main" pull_request: types: - opened From d882db60fc0d9a268aec14c4645e4947eac94783 Mon Sep 17 00:00:00 2001 From: Tyler Chafin Date: Tue, 24 Sep 2024 12:57:47 +0100 Subject: [PATCH 08/17] Update linting.yml --- .github/workflows/linting.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 177172b..19ddb83 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -19,7 +19,7 @@ jobs: - uses: actions/setup-node@v3 - name: Install editorconfig-checker - run: npm install -g editorconfig-checker + run: npm install -g editorconfig-checker@3.0.2 - name: Run ECLint check run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile') From e846b1d215c6aeb76c2831799e5b15b5ffea6e79 Mon Sep 17 00:00:00 2001 From: Tyler Chafin Date: Tue, 24 Sep 2024 13:13:42 +0100 Subject: [PATCH 09/17] Update download_pipeline.yml --- .github/workflows/download_pipeline.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 36fbc9d..9ea6412 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -43,7 +43,7 @@ jobs: architecture: "x64" - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 with: - singularity-version: 3.8.3 + singularity-version: 3.8.7 - name: Install dependencies run: | From d8b32e97aaa948e4b5f6f72b02e221505ef5937f Mon Sep 17 00:00:00 2001 From: Tyler Chafin Date: Tue, 24 Sep 2024 13:22:35 +0100 Subject: [PATCH 10/17] Delete .github/workflows/download_pipeline.yml --- .github/workflows/download_pipeline.yml | 88 ------------------------- 1 file changed, 88 deletions(-) delete mode 100644 .github/workflows/download_pipeline.yml diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml deleted file mode 100644 index 9ea6412..0000000 --- a/.github/workflows/download_pipeline.yml +++ /dev/null @@ -1,88 +0,0 @@ -name: Test successful pipeline download with 'nf-core download' - -# Run the workflow when: -# - dispatched manually -# - when a PR is opened or reopened to master branch -# - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev. -on: - workflow_dispatch: - inputs: - testbranch: - description: "The specific branch you wish to utilize for the test execution of nf-core download." - required: true - default: "main" - pull_request: - types: - - opened - - edited - - synchronize - branches: - - main - - dev - pull_request_target: - branches: - - main - - dev - -env: - NXF_ANSI_LOG: false - -jobs: - download: - runs-on: ubuntu-latest - steps: - - name: Install Nextflow - uses: nf-core/setup-nextflow@v2 - - - name: Disk space cleanup - uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 - with: - python-version: "3.12" - architecture: "x64" - - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 - with: - singularity-version: 3.8.7 - - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install git+https://github.com/nf-core/tools.git@dev - - - name: Get the repository name and current branch set as environment variable - run: | - echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV} - echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} - echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV} - - - name: Download the pipeline - env: - NXF_SINGULARITY_CACHEDIR: ./ - run: | - nf-core download ${{ env.REPO_LOWERCASE }} \ - --revision ${{ env.REPO_BRANCH }} \ - --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ - --compress "none" \ - --container-system 'singularity' \ - --container-library "quay.io" -l "docker.io" -l "ghcr.io" \ - --container-cache-utilisation 'amend' \ - --download-configuration - - - name: Inspect download - run: tree ./${{ env.REPOTITLE_LOWERCASE }} - - - name: Run the downloaded pipeline (stub) - id: stub_run_pipeline - continue-on-error: true - env: - NXF_SINGULARITY_CACHEDIR: ./ - NXF_SINGULARITY_HOME_MOUNT: true - run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results - - name: Run the downloaded pipeline (stub run not supported) - id: run_pipeline - if: ${{ job.steps.stub_run_pipeline.status == failure() }} - env: - NXF_SINGULARITY_CACHEDIR: ./ - NXF_SINGULARITY_HOME_MOUNT: true - run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results From 1db66a4f36ad1d3c00feba8350cce084b7cd7f19 Mon Sep 17 00:00:00 2001 From: Tyler Chafin Date: Tue, 24 Sep 2024 13:29:49 +0100 Subject: [PATCH 11/17] BBtools citation --- subworkflows/local/utils_nfcore_readmapping_pipeline/main.nf | 2 ++ 1 file changed, 2 insertions(+) diff --git a/subworkflows/local/utils_nfcore_readmapping_pipeline/main.nf b/subworkflows/local/utils_nfcore_readmapping_pipeline/main.nf index 92485e0..67a8254 100644 --- a/subworkflows/local/utils_nfcore_readmapping_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_readmapping_pipeline/main.nf @@ -256,6 +256,7 @@ def toolCitationText() { // Uncomment function in methodsDescriptionText to render in MultiQC report def citation_text = [ "Tools used in the workflow included:", + "BBtools (Buschnell 2014),", "blastn (Camacho et al. 2009),", "bwa-mem2 (Vasimuddin et al. 2019),", "Crumble (Bonfield et al. 2019),", @@ -270,6 +271,7 @@ def toolBibliographyText() { // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "
  • Author (2023) Pub name, Journal, DOI
    • " : "", // Uncomment function in methodsDescriptionText to render in MultiQC report def reference_text = [ + "
  • Buschnell, B. (2014). BBtools software package. sourceforge.net/projects/bbmap.
    • ", "
  • Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T.L. (2009). BLAST+: architecture and applications. BMC Bioinformatics, 10, 421. doi:10.1186/1471-2105-10-421.
    • ", "
  • Vasimuddin, Md., Misra, S., Li, H., & Aluru, S. (2019). Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. IEEE Parallel and Distributed Processing Symposium (IPDPS), 2019. doi:10.1109/IPDPS.2019.00041.
    • ", "
  • Bonfield, J.K., McCarthy, S.A., & Durbin, R. (2019). Crumble: reference free lossy compression of sequence quality values. Bioinformatics, 35(2), 337-339. doi:10.1093/bioinformatics/bty608.
    • ", From c687234c3afab37ae31f90210d65081dfc63895f Mon Sep 17 00:00:00 2001 From: Tyler Chafin Date: Wed, 25 Sep 2024 09:39:46 +0100 Subject: [PATCH 12/17] Update CHANGELOG.md Co-authored-by: Matthieu Muffato --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3854131..3630362 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ 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). -## [[1.3.1](https://github.com/sanger-tol/readmapping/releases/tag/1.3.0)] - Antipodean Opaleye - [2024-09-24] +## [[1.3.1](https://github.com/sanger-tol/readmapping/releases/tag/1.3.0)] - Antipodean Opaleye (patch 1) - [2024-09-24] ### Enhancements & fixes From 168dbfc26b1dc5dd28f0f2a28d0526c80811333f Mon Sep 17 00:00:00 2001 From: Tyler Chafin Date: Wed, 25 Sep 2024 09:40:07 +0100 Subject: [PATCH 13/17] Update conf/base.config Co-authored-by: Matthieu Muffato --- conf/base.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/base.config b/conf/base.config index 3827aae..10ab224 100644 --- a/conf/base.config +++ b/conf/base.config @@ -43,7 +43,7 @@ process { // minimum 1GB memory withName: 'BBMAP_FILTERBYNAME' { - memory = { check_max( 1.GB, 'memory' ) } + memory = { check_max( 1.GB * task.attempt, 'memory' ) } } withName: 'SAMTOOLS_COLLATETOFASTA' { From 2f85112c90f5d5716496449cd8f9db3f6d481b40 Mon Sep 17 00:00:00 2001 From: Tyler Chafin Date: Wed, 25 Sep 2024 09:48:34 +0100 Subject: [PATCH 14/17] Update CITATIONS.md --- CITATIONS.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/CITATIONS.md b/CITATIONS.md index 4a33c7c..eb614af 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -10,6 +10,9 @@ ## Pipeline tools +- [BBTools](http://sourceforge.net/projects/bbmap/) + > Bushnell B. BBTools software package. 2014. http://sourceforge.net/projects/bbmap/ + - [Blast](https://pubmed.ncbi.nlm.nih.gov/20003500/) > Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformatics. 2009 Dec 15;10:421. doi: 10.1186/1471-2105-10-421. PMID: 20003500; PMCID: PMC2803857. @@ -18,7 +21,7 @@ > Vasimuddin Md, Misra S, Li H, Aluru S. Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. 2019 IEEE International Parallel and Distributed Processing Symposium. 2019 May;314–24. doi: 10.1109/IPDPS.2019.00041. -- [CRUMBLE] +- [CRUMBLE](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6330002/) > Bonfield JK, McCarthy SA, Durbin R. Crumble: reference free lossy compression of sequence quality values. Bioinformatics. 2019 Jan;35(2):337-339. doi: 10.1093/bioinformatics/bty608. PubMed PMID: 29992288; PMCID: PMC6330002. @@ -30,13 +33,10 @@ > Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H. Twelve years of SAMtools and BCFtools. Gigascience. 2021 Feb 16;10(2):giab008. doi: 10.1093/gigascience/giab008. PMID: 33590861; PMCID: PMC7931819. -- [SeqKit] +- [SeqKit](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5051824/) > Shen W, Le S, Li Y, Hu F. SeqKit: A cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLoS One. 2016 Oct 5;11(10):e0163962. doi: 10.1371/journal.pone.0163962. PubMed PMID: 27706213; PMCID: PMC5051824. -- [Seqtk] - - > Li H. Toolkit for processing sequences in FASTA/Q formats. GitHub Repository. 2012. https://github.com/lh3/seqtk. Accessed August 2024. ## Software packaging/containerisation tools From 485bf9deba4acb4674716ea08cca2c59f7b600b6 Mon Sep 17 00:00:00 2001 From: Tyler Chafin Date: Wed, 25 Sep 2024 09:54:11 +0100 Subject: [PATCH 15/17] prettier linting --- CITATIONS.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CITATIONS.md b/CITATIONS.md index eb614af..c2313c7 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -11,6 +11,7 @@ ## Pipeline tools - [BBTools](http://sourceforge.net/projects/bbmap/) + > Bushnell B. BBTools software package. 2014. http://sourceforge.net/projects/bbmap/ - [Blast](https://pubmed.ncbi.nlm.nih.gov/20003500/) @@ -37,7 +38,6 @@ > Shen W, Le S, Li Y, Hu F. SeqKit: A cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLoS One. 2016 Oct 5;11(10):e0163962. doi: 10.1371/journal.pone.0163962. PubMed PMID: 27706213; PMCID: PMC5051824. - ## Software packaging/containerisation tools - [Anaconda](https://anaconda.com) From ab98d60557e124877e76ab416c4c9bc1b1c6fa09 Mon Sep 17 00:00:00 2001 From: Tyler Chafin Date: Wed, 25 Sep 2024 09:57:11 +0100 Subject: [PATCH 16/17] Update CHANGELOG.md --- CHANGELOG.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3630362..d6c5fc0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,6 +10,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Fixed bug in handling CRAM HiC inputs introduced in 1.1.0 - Fixed bug in handling PacBio FASTQ inputs introduced in 1.3.0 +| Dependency | Old version | New version | +| ---------- | ------------- | ----------- | +| `bbtools` | | 39.01 | +| `seqtk` | 1.4 | | + ## [[1.3.0](https://github.com/sanger-tol/readmapping/releases/tag/1.3.0)] - Antipodean Opaleye - [2024-08-23] ### Enhancements & fixes From 54a11d2ce56c367a08fd2b0a0ba94f261671395e Mon Sep 17 00:00:00 2001 From: Tyler Chafin Date: Wed, 25 Sep 2024 09:58:39 +0100 Subject: [PATCH 17/17] prettier linting --- CHANGELOG.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d6c5fc0..087b1b4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,10 +10,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Fixed bug in handling CRAM HiC inputs introduced in 1.1.0 - Fixed bug in handling PacBio FASTQ inputs introduced in 1.3.0 -| Dependency | Old version | New version | -| ---------- | ------------- | ----------- | -| `bbtools` | | 39.01 | -| `seqtk` | 1.4 | | +| Dependency | Old version | New version | +| ---------- | ----------- | ----------- | +| `bbtools` | | 39.01 | +| `seqtk` | 1.4 | | ## [[1.3.0](https://github.com/sanger-tol/readmapping/releases/tag/1.3.0)] - Antipodean Opaleye - [2024-08-23]