-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
1 parent
816063c
commit bc07e5a
Showing
24 changed files
with
153 additions
and
55 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,13 +1,13 @@ | ||
| report_comment: > | ||
| This report has been generated by the <a href="https://github.com/phac-nml/iridanextexample/releases/tag/dev" target="_blank">phac-nml/iridanextexample</a> | ||
| This report has been generated by the <a href="https://github.com/phac-nml/gasnomenclature/releases/tag/dev" target="_blank">phac-nml/gasnomenclature</a> | ||
| analysis pipeline. For information about how to interpret these results, please see the | ||
| <a href="https://github.com/phac-nml/iridanextexample/" target="_blank">documentation</a>. | ||
| <a href="https://github.com/phac-nml/gasnomenclature/" target="_blank">documentation</a>. | ||
| report_section_order: | ||
| "phac-nml-iridanextexample-methods-description": | ||
| "phac-nml-gasnomenclature-methods-description": | ||
| order: -1000 | ||
| software_versions: | ||
| order: -1001 | ||
| "phac-nml-iridanextexample-summary": | ||
| "phac-nml-gasnomenclature-summary": | ||
| order: -1002 | ||
|
|
||
| export_plots: true |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| # phac-nml/iridanextexample: Output | ||
| # phac-nml/gasnomenclature: Output | ||
|
|
||
| ## Introduction | ||
|
|
||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,37 @@ | ||
|
|
||
|
|
||
| process GAS_CALL{ | ||
| label "process_high" | ||
| tag "Calling: ${meta.id}" | ||
|
|
||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/genomic_address_service%3A0.1.1--pyh7cba7a3_1' : | ||
| 'quay.io/biocontainers/genomic_address_service:0.1.1--pyh7cba7a3_1' }" | ||
|
|
||
|
|
||
| input: | ||
| tuple val(meta), path(reference_clusters), path(distances) | ||
|
|
||
| output: | ||
| tuple val(meta), path("${prefix}/results.{text,parquet}"), emit: distances, optional: true | ||
| tuple val(meta), path("${prefix}/thresholds.json"), emit: thresholds | ||
| tuple val(meta), path("${prefix}/run.json"), emit: run | ||
| path "versions.yml", emit: versions | ||
|
|
||
| script: | ||
| // Need to add more args for gas call below | ||
| prefix = meta.id | ||
| """ | ||
| gas call --dists $distances \\ | ||
| --rclusters $reference_clusters \\ | ||
| --outdir ${prefix} \\ | ||
| --threshold ${params.gm_thresholds} \\ | ||
| --delimeter ${params.gm_delimiter} | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| genomic_address_service: \$( gas call -V | sed -e "s/gas//g" ) | ||
| END_VERSIONS | ||
| """ | ||
|
|
||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,61 @@ | ||
| process PROFILE_DISTS{ | ||
| label "process_high" | ||
| tag "Pairwise Distance Generation: ${meta.id}" | ||
|
|
||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/profile_dists%3A1.0.0--pyh7cba7a3_0' : | ||
| 'quay.io/biocontainers/profile_dists:1.0.0--pyh7cba7a3_0' }" | ||
|
|
||
| input: | ||
| tuple val(meta), path(query), path(ref) | ||
| val mapping_format | ||
| path(mapping_file) | ||
| path(columns) | ||
|
|
||
|
|
||
| output: | ||
| tuple val(meta), path("${prefix}_${mapping_format}/allele_map.json"), emit: allele_map | ||
| tuple val(meta), path("${prefix}_${mapping_format}/query_profile.{text,parquet}"), emit: query_profile | ||
| tuple val(meta), path("${prefix}_${mapping_format}/ref_profile.{text,parquet}"), emit: ref_profile | ||
| tuple val(meta), path("${prefix}_${mapping_format}/results.{text,parquet}"), emit: results | ||
| tuple val(meta), path("${prefix}_${mapping_format}/run.json"), emit: run | ||
| path "versions.yml", emit: versions | ||
|
|
||
|
|
||
| script: | ||
| def args = "" | ||
|
|
||
| if(mapping_file){ | ||
| args = args + "--mapping_file $mapping_file" | ||
| } | ||
| if(columns){ | ||
| args = args + " --columns $columns" | ||
| } | ||
| if(params.pd_force){ | ||
| args = args + " --force" | ||
| } | ||
| if(params.pd_skip){ | ||
| args = args + " --skip" | ||
| } | ||
| if(params.pd_count_missing){ | ||
| args = args + " --count_missing" | ||
| } | ||
| // --match_threshold $params.profile_dists.match_thresh \\ | ||
| prefix = meta.id | ||
| """ | ||
| profile_dists --query $query --ref $ref $args --outfmt $mapping_format \\ | ||
| --distm $params.pd_distm \\ | ||
| --file_type $params.pd_file_type \\ | ||
| --missing_thresh $params.pd_missing_threshold \\ | ||
| --sample_qual_thresh $params.pd_sample_quality_threshold \\ | ||
| --max_mem ${task.memory.toGiga()} \\ | ||
| --cpus ${task.cpus} \\ | ||
| -o ${prefix}_${mapping_format} | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| profile_dists: \$( profile_dists -V | sed -e "s/profile_dists//g" ) | ||
| END_VERSIONS | ||
| """ | ||
|
|
||
| } |
Oops, something went wrong.