diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 5f1b621..02f7106 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\|cff\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile') diff --git a/LICENSE b/LICENSE index ce98c0b..257404f 100755 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,8 @@ MIT License -Copyright (c) Damon-Lee B Pointon (@DLBPointon) +Copyright (c) 2022-2024 Genome Research Ltd. +except `bin/filter_five_end.pl`: +Copyright (c) 2017 Arima Genomics, Inc. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal @@ -19,8 +21,3 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - - -The filter_five_end.ph script has been taken from the Arima Mapping Pipeline, has not been modified and is subject to the below license: - -Copyright (c) 2017 Arima Genomics, Inc. diff --git a/README.md b/README.md index 32dc1f2..c4771c1 100755 --- a/README.md +++ b/README.md @@ -47,6 +47,10 @@ Currently, the pipeline uses the following flags: - The directory of the cram _and_ cram.crai files, e.g., `/path/to/cram/` +- `--map_order` + + - hic map scaffold order, input either `length` or `unsorted` + - `--teloseq` - A telomeric sequence, e.g., `TTAGGG` @@ -66,7 +70,8 @@ nextflow run sanger-tol/curationpretext \ --longread { path/to/longread/fasta/ } \ --longread_type { default is "hifi" } --sample { default is "pretext_rerun" } \ - --teloseq { deafault is "TTAGGG" } \ + --teloseq { default is "TTAGGG" } \ + --map_order { default is "unsorted" } \ --outdir { OUTDIR } \ -profile @@ -81,7 +86,8 @@ nextflow run sanger-tol/curationpretext \ --longread { path/to/longread/fasta/ } \ --longread_type { default is "hifi" } --sample { default is "pretext_rerun" } \ - --teloseq { deafault is "TTAGGG" } \ + --teloseq { default is "TTAGGG" } \ + --map_order { default is "unsorted" } \ --outdir { OUTDIR } \ -profile \ -entry MAPS_ONLY \ diff --git a/bin/find_telomere b/bin/find_telomere deleted file mode 100755 index b7d84a1..0000000 Binary files a/bin/find_telomere and /dev/null differ diff --git a/conf/modules.config b/conf/modules.config index 90e2412..33b7601 100755 --- a/conf/modules.config +++ b/conf/modules.config @@ -133,12 +133,12 @@ process { } withName: PRETEXTMAP_STANDRD { - ext.args = { "--sortby length --mapq 0 --memory ${task.memory.giga}G" } + ext.args = { "${meta.map_order.equals("length") ? "--sortby length": "--sortby nosort" } --mapq 0 --memory ${task.memory.giga}" } ext.prefix = { "${meta.id}_normal_pi" } } withName: PRETEXTMAP_HIGHRES { - ext.args = { "--sortby length --highRes --mapq 0 --memory ${task.memory.giga}G" } + ext.args = { "${meta.map_order.equals("length") ? "--sortby length": "--sortby nosort" } --highRes --mapq 0" } ext.prefix = { "${meta.id}_hr_pi" } } diff --git a/modules/local/find_telomere_regions.nf b/modules/local/find_telomere_regions.nf index 8a37153..223ab41 100755 --- a/modules/local/find_telomere_regions.nf +++ b/modules/local/find_telomere_regions.nf @@ -2,7 +2,7 @@ process FIND_TELOMERE_REGIONS { tag "${meta.id}" label 'process_low' - container 'docker.io/library/gcc:7.1.0' + container 'quay.io/sanger-tol/telomere:0.0.1-c1' // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { diff --git a/nextflow.config b/nextflow.config index 8a2504e..8faa3d3 100755 --- a/nextflow.config +++ b/nextflow.config @@ -17,6 +17,7 @@ params { cram = null aligner = "bwamem2" longread_type = "hifi" + map_order = "unsorted" // Boilerplate options outdir = "${params.outdir}/results" diff --git a/nextflow_schema.json b/nextflow_schema.json index 3bf2f07..9737735 100755 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -10,7 +10,7 @@ "type": "object", "fa_icon": "fas fa-terminal", "description": "Define where the pipeline should find input data and save output data.", - "required": ["input", "cram", "sample", "outdir"], + "required": ["input", "cram", "sample", "outdir", "map_order"], "properties": { "input": { "type": "string", @@ -46,6 +46,12 @@ "help_text": "Give me a telomeric motif", "fa_icon": "fas fa-file-signature" }, + "map_order": { + "type": "string", + "description": "HiC map scaffold order. Default to unsorted", + "help_text": "How you want to display your hic map, sorted by length?", + "fa_icon": "fas fa-file-signature" + }, "aligner": { "type": "string", "description": "Aligner for use {minimap2, bwamem2} in generating map", diff --git a/subworkflows/local/generate_maps.nf b/subworkflows/local/generate_maps.nf index 440492a..3b5b2ed 100755 --- a/subworkflows/local/generate_maps.nf +++ b/subworkflows/local/generate_maps.nf @@ -20,6 +20,7 @@ workflow GENERATE_MAPS { reference_tuple // Channel [ val(meta), path(file) ] hic_reads_path // Channel [ val(meta), path(directory) ] + main: ch_versions = Channel.empty()