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| variables: | ||
| GIT_SUBMODULE_STRATEGY: "recursive" | ||
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| image: "${CI_REGISTRY}/bioinfo-containers/deploy-geniac:master" | ||
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| stages: | ||
| - check # check that requirements are met | ||
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| before_script: | ||
| - set -euo pipefail | ||
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| ############################# | ||
| # Perform preliminary check # | ||
| ############################# | ||
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| geniac_lint: | ||
| # launch geniac lint | ||
| stage: check | ||
| script: | ||
| - echo "Geniac lint" | ||
| - source /opt/etc/bashrc # needed to activate the geniac conda env | ||
| - geniac --version | ||
| - geniac lint ${CI_PROJECT_DIR} | ||
| tags: | ||
| - rancher | ||
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| @@ -1,11 +1,11 @@ | ||
| ======================================================================== | ||
| ------------------------------------------------------------------------${reset}${yellow} | ||
| DISCLAIMER | ||
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| This software is currently under active development and the results | ||
| have been generated with a non stable version. | ||
| The reliability, reproducibility and the quality of the results are | ||
| therefore not guaranteed. | ||
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| /!\ Do not use the results for any kind of projects /!\ | ||
| ======================================================================== | ||
| /!\\ Do not use the results for any kind of projects /!\\ | ||
| ${reset}------------------------------------------------------------------------ | ||
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| @@ -1,35 +1,50 @@ | ||
| ---------------------------------------------------- | ||
| ${workflowName} v${version} | ||
| ---------------------------------------------------- | ||
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| Run Name: $runName | ||
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| <% if (success){ | ||
| out << "## ${workflowName} execution completed successfully! ##" | ||
| <html> | ||
| <head> | ||
| <head> | ||
| <meta charset="utf-8"> | ||
| <meta http-equiv="X-UA-Compatible" content="IE=edge"> | ||
| <meta name="viewport" content="width=device-width, initial-scale=1"> | ||
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| <meta name="description" content="Nextflow analysis pipeline (Institut Curie)"> | ||
| <title>Pipeline Report</title> | ||
| </head> | ||
| <body> | ||
| <div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto;"> | ||
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| <h1>${workflowName} v${version}</h1> | ||
| <h2>Run Name: $runName</h2> | ||
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| <% if (!success){ | ||
| out << """ | ||
| <div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;"> | ||
| <h4 style="margin-top:0; color: inherit;">execution completed unsuccessfully!</h4> | ||
| <p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p> | ||
| <p>The full error message was:</p> | ||
| <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre> | ||
| </div> | ||
| """ | ||
| } else { | ||
| out << """#################################################### | ||
| ## ${workflowName} execution completed unsuccessfully! ## | ||
| #################################################### | ||
| The exit status of the task that caused the workflow execution to fail was: $exitStatus. | ||
| The full error message was: | ||
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| ${errorReport} | ||
| """ | ||
| }%> | ||
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| The workflow was completed at $dateComplete (duration: $duration) | ||
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| The command used to launch the workflow was as follows: | ||
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| $commandLine | ||
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| Pipeline Configuration: | ||
| ----------------------- | ||
| <% out << summary.collect{ k,v -> " - $k: $v" }.join("\n") %> | ||
| out << """ | ||
| <div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;"> | ||
| execution completed successfully! | ||
| </div> | ||
| """ | ||
| } | ||
| %> | ||
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| <p>The workflow was completed at <strong>$dateComplete</strong> (duration: <strong>$duration</strong>)</p> | ||
| <p>The command used to launch the workflow was as follows:</p> | ||
| <pre style="white-space: pre-wrap; overflow: visible; background-color: #ededed; padding: 15px; border-radius: 4px; margin-bottom:30px;">$commandLine</pre> | ||
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| <h3>Pipeline Configuration:</h3> | ||
| <table style="width:100%; max-width:100%; border-spacing: 0; border-collapse: collapse; border:0; margin-bottom: 30px;"> | ||
| <tbody style="border-bottom: 1px solid #ddd;"> | ||
| <% out << summary.collect{ k,v -> "<tr><th style='text-align:left; padding: 8px 0; line-height: 1.42857143; vertical-align: top; border-top: 1px solid #ddd;'>$k</th><td style='text-align:left; padding: 8px; line-height: 1.42857143; vertical-align: top; border-top: 1px solid #ddd;'><pre style='white-space: pre-wrap; overflow: visible;'>$v</pre></td></tr>" }.join("\n") %> | ||
| </tbody> | ||
| </table> | ||
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| </div> | ||
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| </body> | ||
| </html> | ||
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| -- | ||
| ${workflowName} | ||
| ${url} |
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| ## Describe the fields | ||
| ## For definition, provide the expected key:values | ||
| ## Note that several keys/values can be defined | ||
| ## | ||
| ############################################### | ||
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| freq: 'AF' | ||
| depth: 'DP' | ||
| altDepth: 'AD' |
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| ## Describe the fields | ||
| ## For definition, provide the expected key:values | ||
| ## Note that several keys/values can be defined | ||
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| ############################################### | ||
| ## SnpEff Parsing | ||
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| ## Tags | ||
| tag: 'ANN' | ||
| sep: '&' | ||
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| ## Annotation flags | ||
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| isCoding: | ||
| 1: | ||
| - chromosome_number_variation | ||
| - coding_sequence_variant | ||
| - conservative_inframe_deletion | ||
| - conservative_inframe_insertion | ||
| - disruptive_inframe_deletion | ||
| - disruptive_inframe_insertion | ||
| - exon_loss | ||
| - exon_loss_variant | ||
| - exon_variant | ||
| - frameshift_variant | ||
| - gene_variant | ||
| - initiator_codon_variant | ||
| - missense_variant | ||
| - rare_amino_acid_variant | ||
| - splice_acceptor_variant | ||
| - splice_donor_variant | ||
| - splice_region_variant | ||
| - start_lost | ||
| - start_retained | ||
| - stop_gained | ||
| - stop_lost | ||
| - stop_retained_variant | ||
| - synonymous_variant | ||
| - transcript_ablation | ||
| - transcript_amplification | ||
| - transcript_variant | ||
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| isNonCoding: | ||
| 1: | ||
| - 3_prime_UTR_truncation | ||
| - 3_prime_UTR_variant | ||
| - 5_prime_UTR_premature_start_codon_gain_variant | ||
| - 5_prime_UTR_truncation | ||
| - 5_prime_UTR_variant | ||
| - conserved_intergenic_variant | ||
| - conserved_intron_variant | ||
| - downstream_gene_variant | ||
| - feature_elongation | ||
| - feature_truncation | ||
| - intergenic_region | ||
| - intragenic_variant | ||
| - intron_variant | ||
| - mature_miRNA_variant | ||
| - miRNA | ||
| - NMD_transcript_variant | ||
| - non_coding_transcript_exon_variant | ||
| - non_coding_transcript_variant | ||
| - regulatory_region_ablation | ||
| - regulatory_region_amplification | ||
| - regulatory_region_variant | ||
| - TF_binding_site_variant | ||
| - TFBS_ablation | ||
| - TFBS_amplification | ||
| - upstream_gene_variant | ||
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| isSplicing: | ||
| 1: | ||
| - splice_donor_variant | ||
| - splice_acceptor_variant | ||
| - splice_region_variant | ||
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| isSynonymous: | ||
| 1: | ||
| - start_retained_variant | ||
| - stop_retained_variant | ||
| - synonymous_variant | ||
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| isNonSynonymous: | ||
| 1: | ||
| - frameshift_variant | ||
| - missense_variant | ||
| - rare_amino_acid_variant | ||
| - splice_acceptor_variant | ||
| - splice_donor_variant | ||
| - splice_region_variant | ||
| - start_lost | ||
| - stop_gained | ||
| - stop_lost | ||
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| ## Databases | ||
| cancerDb: | ||
| cosmic: | ||
| - COSMIC | ||
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| polymDb: | ||
| 1k: | ||
| - kg_AMR_AF | ||
| - kg_AFR_AF | ||
| - kg_EAS_AF | ||
| - kg_EUR_AF | ||
| - kg_SAS_AF | ||
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| gnomad: | ||
| - AF |
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