From 7335c1967b5c13b6dc8da0519d7d3a40cc4484e9 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 21 May 2024 10:30:34 +0200 Subject: [PATCH 1/2] add tools docs images to rich-codex.yml --- .github/rich-codex.yml | 198 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 198 insertions(+) diff --git a/.github/rich-codex.yml b/.github/rich-codex.yml index 65ffaf5531..386663b4ee 100644 --- a/.github/rich-codex.yml +++ b/.github/rich-codex.yml @@ -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 "nf-core_bot@example.com" && \ + 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 From 59120ee59b40b5923e0ea8b646076fd8599e71f1 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 21 May 2024 08:39:19 +0000 Subject: [PATCH 2/2] [automated] Fix code linting --- .github/rich-codex.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/rich-codex.yml b/.github/rich-codex.yml index 386663b4ee..2e4a1aa34b 100644 --- a/.github/rich-codex.yml +++ b/.github/rich-codex.yml @@ -62,7 +62,7 @@ outputs: img_paths: - public/images/tools/nf-core-list-stars.svg - command: nf-core launch rnaseq -r 3.8.1 - trim_after: "Command line" + 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