Update WDLs for upcoming pVACtools 4.0.0 release #93
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tmooney
reviewed
Mar 13, 2023
definitions/tools/pvacfuse.wdl
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| } | ||
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| Int space_needed_gb = 10 + round(size([input_fusions_zip], "GB") * 3) | ||
| runtime { | ||
| preemptible: 1 | ||
| maxRetries: 2 | ||
| docker: "griffithlab/pvactools:3.1.0" | ||
| docker: "susannakiwala/pvactools:4.0.0_rc_pvacview_v3" |
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Just commenting to note that we'll want to replace this with the final release version once it's ready.
tmooney
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Mar 13, 2023
susannasiebert
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malachig
reviewed
Apr 21, 2023
| ~{if defined(iedb_retries) then "-r ~{iedb_retries}" else ""} \ | ||
| ~{if keep_tmp_files then "-k" else ""} \ | ||
| ~{if defined(normal_sample_name) then "--normal-sample-name ~{normal_sample_name}" else ""} \ | ||
| ~{if defined(net_chop_method) then "--net-chop-method ~{net_chop_method}" else ""} \ | ||
| ~{if netmhc_stab then "--netmhc-stab" else ""} \ | ||
| ~{if run_reference_proteome_similarity then "--run-reference-proteome-similarity" else ""} \ | ||
| ~{if defined(peptide_fasta) then "--peptide-fasta ~{peptide_fasta}" else ""} \ | ||
| ~{if defined(top_score_metric) then "-m ~{top_score_metric}" else ""} \ | ||
| ~{if defined(net_chop_threshold) then "--net-chop-threshold ~{net_chop_threshold}" else ""} \ | ||
| ~{if defined(additional_report_columns) then "-m ~{additional_report_columns}" else ""} \ |
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It looks like -m is here twice?
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This all seems to be working as expected in my test with real datasets. |
malachig
reviewed
Apr 24, 2023
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