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Merge pull request #2528 from mirpedrol/tools-images
add tools docs images to rich-codex.yml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -50,3 +50,201 @@ outputs: | |
| fake_command: nf-core modules create fastqc --author @janedoe --label process_low --meta | ||
| img_paths: | ||
| - public/images/contributing/modules/nf-core-modules-create.svg | ||
| - commmand: nf-core list | ||
| head: 19 | ||
| img_paths: | ||
| - public/images/tools/nf-core-list.svg | ||
| - commmand: nf-core list rna rna-seq | ||
| img_paths: | ||
| - public/images/tools/nf-core-list-rna.svg | ||
| - commmand: nf-core list -s stars | ||
| head: 18 | ||
| img_paths: | ||
| - public/images/tools/nf-core-list-stars.svg | ||
| - command: nf-core launch rnaseq -r 3.8.1 | ||
| trim_after: 'Command line' | ||
| img_paths: | ||
| - public/images/tools/nf-core-launch-rnaseq.svg | ||
| - commmand: mkdir tmp && cd tmp && nf-core download rnaseq -r 3.8 --outdir nf-core-rnaseq -x none -s none -d | ||
| img_paths: | ||
| - public/images/tools/nf-core-download.svg | ||
| - command: cd tmp && tree -L 2 nf-core-rnaseq/ | ||
| img_paths: | ||
| - public/images/tools/nf-core-download-tree.svg | ||
| - command: nf-core licences deepvariant | ||
| timeout: 10 | ||
| img_paths: | ||
| - public/images/tools/nf-core-licences.svg | ||
| - command: cd tmp && nf-core create -n nextbigthing -d "This pipeline analyses data from the next big omics technique" -a "Big Steve" --plain | ||
| fake_command: nf-core create -n nextbigthing -d "This pipeline analyses data from the next big omics technique" -a "Big Steve" --plain | ||
| img_paths: | ||
| - public/images/tools/nf-core-create.svg | ||
| - command: | | ||
| cd tmp/nf-core-nextbigthing && \ | ||
| echo "lint: { pipeline_todos: false }" >> .nf-core.yml && \ | ||
| nf-core lint | ||
| fake_command: nf-core lint | ||
| img_paths: | ||
| - public/images/tools/nf-core-lint.svg | ||
| - command: | | ||
| cd tmp && \ | ||
| echo "{input: myfiles.csv, outdir: results}" > nf-params.json | ||
| nf-core schema validate nf-core-rnaseq/3_8 nf-params.json | ||
| timeout: 10 | ||
| fake_command: nf-core schema validate nf-core-rnaseq/3_8 nf-params.json | ||
| after_command: rm nf-params.json | ||
| img_paths: | ||
| - public/images/tools/nf-core-schema-validate.svg | ||
| - command: | | ||
| cd tmp/nf-core-nextbigthing && \ | ||
| sed '25,30d' nextflow_schema.json > nextflow_schema.json.tmpsed '25,30d' nextflow_schema.json > nextflow_schema.json.tmp && \ | ||
| mv nextflow_schema.json.tmp nextflow_schema.json && \ | ||
| nf-core schema build --no-prompts | ||
| timeout: 10 | ||
| fake_command: nf-core schema build --no-prompts | ||
| img_paths: | ||
| - public/images/tools/nf-core-schema-build.svg | ||
| - command: cd tmp/nf-core-nextbigthing && nf-core schema lint | ||
| fake_command: nf-core schema lint | ||
| img_paths: | ||
| - public/images/tools/nf-core-schema-lint.svg | ||
| - command: cd tmp/nf-core-nextbigthing && nf-core bump-version 1.1 | ||
| fake_command: nf-core bump-version 1.1 | ||
| img_paths: | ||
| - public/images/tools/nf-core-bump-version.svg | ||
| - command: | | ||
| cd tmp/nf-core-nextbigthing && \ | ||
| git config --global user.email "[email protected]" && \ | ||
| git config --global user.name "nf-core_bot" && \ | ||
| git commit -am "Bump version" && \ | ||
| nf-core sync | ||
| fake_command: nf-core sync | ||
| img_paths: | ||
| - public/images/tools/nf-core-sync.svg | ||
| - command: cd tmp && nf-core create-logo nextbigthing | ||
| fake_command: nf-core create-logo nextbigthing | ||
| img_paths: | ||
| - public/images/tools/nf-core-create-logo.svg | ||
| - command: cd tmp/nf-core-nextbigthing && nf-core modules list remote | ||
| head: 25 | ||
| fake_command: nf-core modules list remote | ||
| img_paths: | ||
| - public/images/tools/nf-core-modules-list-remote.svg | ||
| - command: cd tmp/nf-core-nextbigthing && nf-core modules list local | ||
| head: 25 | ||
| fake_command: nf-core modules list local | ||
| img_paths: | ||
| - public/images/tools/nf-core-modules-list-local.svg | ||
| - command: cd tmp/nf-core-nextbigthing && nf-core modules info abacas | ||
| fake_command: nf-core modules info abacas | ||
| img_paths: | ||
| - public/images/tools/nf-core-modules-info.svg | ||
| - command: cd tmp/nf-core-nextbigthing && nf-core modules install abacas | ||
| fake_command: nf-core modules install abacas | ||
| img_paths: | ||
| - public/images/tools/nf-core-modules-install.svg | ||
| - command: cd tmp/nf-core-nextbigthing && nf-core modules update --all --no-preview | ||
| fake_command: nf-core modules update --all --no-preview | ||
| img_paths: | ||
| - public/images/tools/nf-core-modules-update.svg | ||
| - command: cd tmp/nf-core-nextbigthing && nf-core modules remove abacas | ||
| fake_command: nf-core modules remove abacas | ||
| img_paths: | ||
| - public/images/tools/nf-core-modules-remove.svg | ||
| - command: | | ||
| cd tmp/nf-core-nextbigthing && \ | ||
| sed "s/process_medium/process_low/g" modules/nf-core/fastqc/main.nf > modules/nf-core/fastqc/main.nf.patch && \ | ||
| mv modules/nf-core/fastqc/main.nf.patch modules/nf-core/fastqc/main.nf && \ | ||
| nf-core modules patch fastqc | ||
| fake_command: nf-core modules patch fastqc | ||
| img_paths: | ||
| - public/images/tools/nf-core-modules-patch.svg | ||
| - command: | | ||
| cd tmp && \ | ||
| git clone https://github.com/nf-core/modules.git && cd modules && \ | ||
| nf-core modules create fastqc --author @nf-core-bot --label process_low --meta --force | ||
| timeout: 10 | ||
| fake_command: nf-core modules create fastqc --author @nf-core-bot --label process_low --meta --force | ||
| img_paths: | ||
| - public/images/tools/nf-core-modules-create.svg | ||
| - command: | | ||
| cd tmp/modules && \ | ||
| sed 's/1.13a/1.10/g' modules/multiqc/main.nf > modules/multiqc/main.nf.tmp && \ | ||
| mv modules/multiqc/main.nf.tmp modules/multiqc/main.nf && \ | ||
| nf-core modules lint multiqc | ||
| fake_command: nf-core modules lint multiqc | ||
| img_paths: | ||
| - public/images/tools/nf-core-modules-lint.svg | ||
| - command: cd tmp/modules && nf-core modules test fastqc --no-prompts | ||
| timeout: 30 | ||
| extra_env: | ||
| PROFILE: 'conda' | ||
| fake_command: nf-core modules test fastqc --no-prompts | ||
| img_paths: | ||
| - public/images/tools/nf-core-modules-test.svg | ||
| - command: cd tmp/modules && nf-core modules bump-version fastqc | ||
| fake_command: nf-core modules bump-version fastqc | ||
| img_paths: | ||
| - public/images/tools/nf-core-modules-bump-version.svg | ||
| - command: cd tmp/nf-core-nextbigthing && nf-core subworkflows list remote | ||
| head: 25 | ||
| fake_command: nf-core subworkflows list remote | ||
| img_paths: | ||
| - public/images/tools/nf-core-subworkflows-list-remote.svg | ||
| - command: | | ||
| cd tmp/nf-core-nextbigthing && \ | ||
| echo "repository_type: pipeline" >> .nf-core.yml && \ | ||
| nf-core subworkflows list local | ||
| head: 25 | ||
| fake_command: nf-core subworkflows list local | ||
| img_paths: | ||
| - public/images/tools/nf-core-subworkflows-list-local.svg | ||
| - command: | | ||
| cd tmp/nf-core-nextbigthing && \ | ||
| echo "repository_type: pipeline" >> .nf-core.yml && \ | ||
| nf-core subworkflows info bam_rseqc | ||
| head: 15 | ||
| tail: 10 | ||
| fake_command: nf-core subworkflows info bam_rseqc | ||
| img_paths: | ||
| - public/images/tools/nf-core-subworkflows-info.svg | ||
| - command: | | ||
| cd tmp/nf-core-nextbigthing && \ | ||
| echo "repository_type: pipeline" >> .nf-core.yml && \ | ||
| nf-core subworkflows install bam_rseqc | ||
| fake_command: nf-core subworkflows install bam_rseqc | ||
| img_paths: | ||
| - public/images/tools/nf-core-subworkflows-install.svg | ||
| - command: | | ||
| cd tmp/nf-core-nextbigthing && \ | ||
| echo "repository_type: pipeline" >> .nf-core.yml && \ | ||
| nf-core subworkflows update --all --no-preview | ||
| timeout: 30 | ||
| fake_command: nf-core subworkflows update --all --no-preview | ||
| img_paths: | ||
| - public/images/tools/nf-core-subworkflows-update.svg | ||
| - command: | | ||
| cd tmp/nf-core-nextbigthing && \ | ||
| echo "repository_type: pipeline" >> .nf-core.yml && \ | ||
| nf-core subworkflows remove bam_rseqc | ||
| fake_command: nf-core subworkflows remove bam_rseqc | ||
| img_paths: | ||
| - public/images/tools/nf-core-subworkflows-remove.svg | ||
| - command: | | ||
| cd tmp/modules && \ | ||
| nf-core subworkflows create bam_stats_samtools --author @nf-core-bot --force | ||
| img_paths: | ||
| - public/images/tools/nf-core-subworkflows-create.svg | ||
| - command: cd tmp/modules && nf-core subworkflows test bam_rseqc --no-prompts | ||
| timeout: 30 | ||
| extra_env: | ||
| PROFILE: 'conda' | ||
| fake_command: nf-core subworkflows test bam_rseqc --no-prompts | ||
| img_paths: | ||
| - public/images/tools/nf-core-subworkflows-test.svg | ||
| - command: cd tmp/modules && nf-core subworkflows lint bam_stats_samtools | ||
| extra_env: | ||
| PROFILE: 'conda' | ||
| fake_command: nf-core subworkflows lint bam_stats_samtools | ||
| img_paths: | ||
| - public/images/tools/nf-core-subworkflows-lint.svg | ||