| Previous changeset 31:1117def5cd24 (2024-12-04) Next changeset 33:6f4e6377ba64 (2024-12-05) |
|
Commit message:
"planemo upload" |
|
modified:
CSP2/conf/profiles.config csp2_snp.xml |
| CSP2/conf/profiles.config |
| diff -r 1117def5cd24 -r a12953834916 CSP2/conf/profiles.config |
| CSP2/conf/profiles.config |
| --- a/CSP2/conf/profiles.config Wed Dec 04 19:08:38 2024 -0500 +++ b/CSP2/conf/profiles.config Thu Dec 05 10:47:01 2024 -0500 @@ -85,7 +85,7 @@ conda.cacheDir = "${projectDir}/CSP2_env" process.conda = "${projectDir}/conf/CSP2.yaml" - process.queue = "ondemand-small" + process.queue = "q8cpu" executor.$slurm.exitReadTimeout = 120000 |
| csp2_snp.xml |
| diff -r 1117def5cd24 -r a12953834916 csp2_snp.xml |
| csp2_snp.xml |
| --- a/csp2_snp.xml Wed Dec 04 19:08:38 2024 -0500 +++ b/csp2_snp.xml Thu Dec 05 10:47:01 2024 -0500 @@ -95,20 +95,21 @@ <data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="Nextflow_Log.txt" /> <data name="csp2_zip" format="zip" label="Zipped Output" from_work_dir="CSP2_Output.zip" /> - <collection name="snp_analysis_results" type="list:dataset" label="SNP Analysis Results by Reference ID"> - <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/CSP2_SNP_Pipeline.log" format="txt" /> - <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snplist.txt" format="txt" /> - <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snplist_preserved.txt" format="txt" /> - <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/Reference_Screening.tsv" format="tabular" /> - <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/Locus_Categories.tsv" format="tabular" /> - <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/Query_Coverage.tsv" format="tabular" /> - <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snp_distance_matrix_preserved.tsv" format="tabular" /> - <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snp_distance_matrix.tsv" format="tabular" /> - <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snp_distance_pairwise_preserved.tsv" format="tabular" /> - <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snp_distance_pairwise.tsv" format="tabular" /> - <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snpma_preserved.fasta" format="fasta" /> - <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snpma.fasta" format="fasta" /> + <collection name="snp_pipeline_output" type="list"> + <discover_datasets pattern="(?P<reference_id>.+)/CSP2_SNP_Pipeline\.log" ext="txt" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" /> + <discover_datasets pattern="(?P<reference_id>.+)/snplist\.txt" ext="txt" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" /> + <discover_datasets pattern="(?P<reference_id>.+)/snplist_preserved\.txt" ext="txt" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" /> + <discover_datasets pattern="(?P<reference_id>.+)/Reference_Screening\.tsv" ext="tabular" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" /> + <discover_datasets pattern="(?P<reference_id>.+)/Locus_Categories\.tsv" ext="tabular" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" /> + <discover_datasets pattern="(?P<reference_id>.+)/Query_Coverage\.tsv" ext="tabular" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" /> + <discover_datasets pattern="(?P<reference_id>.+)/snp_distance_matrix_preserved\.tsv" ext="tabular" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" /> + <discover_datasets pattern="(?P<reference_id>.+)/snp_distance_matrix\.tsv" ext="tabular" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" /> + <discover_datasets pattern="(?P<reference_id>.+)/snp_distance_pairwise_preserved\.tsv" ext="tabular" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" /> + <discover_datasets pattern="(?P<reference_id>.+)/snp_distance_pairwise\.tsv" ext="tabular" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" /> + <discover_datasets pattern="(?P<reference_id>.+)/snpma_preserved\.fasta" ext="fasta" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" /> + <discover_datasets pattern="(?P<reference_id>.+)/snpma\.fasta" ext="fasta" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" /> </collection> + </outputs> <tests> <test> |