From 757f31696cc4454c734657d52c91a8ba3317965f Mon Sep 17 00:00:00 2001 From: Michal Babinski Date: Tue, 22 Oct 2024 08:50:32 -0400 Subject: [PATCH] [MerlinMagic] Fixed output for crypto snippy_variants_num_variants (#654) * fix num variants output for crypto * updated md5 for merlin magic * updates to md5 sum --------- Co-authored-by: Sage Wright --- tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml | 2 +- tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml | 2 +- workflows/utilities/wf_merlin_magic.wdl | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml index d44afed4a..91ae801b7 100644 --- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml +++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml @@ -633,7 +633,7 @@ - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl md5sum: 6d9dd969e2144ca23f2a0e101e6b6966 - path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl - md5sum: cb2e4068f574b9fe7307b19a6437ce43 + md5sum: 670f990128063eb3c7b3fa49302f08b7 - path: miniwdl_run/wdl/workflows/utilities/wf_read_QC_trim_pe.wdl contains: ["version", "QC", "output"] - path: miniwdl_run/workflow.log diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml index adeb6971f..82f9a9a74 100644 --- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml +++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml @@ -596,7 +596,7 @@ - path: miniwdl_run/wdl/workflows/theiaprok/wf_theiaprok_illumina_se.wdl md5sum: 5aa25e4fad466f92c96a7c138aca0d20 - path: miniwdl_run/wdl/workflows/utilities/wf_merlin_magic.wdl - md5sum: cb2e4068f574b9fe7307b19a6437ce43 + md5sum: 670f990128063eb3c7b3fa49302f08b7 - path: miniwdl_run/wdl/workflows/utilities/wf_read_QC_trim_se.wdl md5sum: d11bfe33fdd96eab28892be5a01c1c7d - path: miniwdl_run/workflow.log diff --git a/workflows/utilities/wf_merlin_magic.wdl b/workflows/utilities/wf_merlin_magic.wdl index 2bc25eebf..1d6914e79 100644 --- a/workflows/utilities/wf_merlin_magic.wdl +++ b/workflows/utilities/wf_merlin_magic.wdl @@ -976,7 +976,7 @@ workflow merlin_magic { String snippy_variants_summary = select_first([snippy_cauris.snippy_variants_summary, snippy_afumigatus.snippy_variants_summary, snippy_crypto.snippy_variants_summary, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"]) String snippy_variants_num_reads_aligned = select_first([snippy_cauris.snippy_variants_num_reads_aligned, snippy_afumigatus.snippy_variants_num_reads_aligned, snippy_crypto.snippy_variants_num_reads_aligned, "No matching taxon detected"]) String snippy_variants_coverage_tsv = select_first([snippy_cauris.snippy_variants_coverage_tsv, snippy_afumigatus.snippy_variants_coverage_tsv, snippy_crypto.snippy_variants_coverage_tsv, "gs://theiagen-public-files/terra/theiaeuk_files/no_match_detected.txt"]) - String snippy_variants_num_variants = select_first([snippy_cauris.snippy_variants_num_variants, snippy_afumigatus.snippy_variants_num_variants, snippy_crypto.snippy_variants_num_reads_aligned, "No matching taxon detected"]) + String snippy_variants_num_variants = select_first([snippy_cauris.snippy_variants_num_variants, snippy_afumigatus.snippy_variants_num_variants, snippy_crypto.snippy_variants_num_variants, "No matching taxon detected"]) String snippy_variants_percent_ref_coverage = select_first([snippy_cauris.snippy_variants_percent_ref_coverage, snippy_afumigatus.snippy_variants_percent_ref_coverage, snippy_crypto.snippy_variants_percent_ref_coverage, "No matching taxon detected"]) } } \ No newline at end of file