From 1f82443ea8df5092e7d0c0077825ed4a7e6fb937 Mon Sep 17 00:00:00 2001 From: Michal-Babins Date: Fri, 18 Oct 2024 18:27:19 +0000 Subject: [PATCH 1/3] fix num variants output for crypto --- workflows/utilities/wf_merlin_magic.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/utilities/wf_merlin_magic.wdl b/workflows/utilities/wf_merlin_magic.wdl index 690086a60..700e8c8eb 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 From ffd63fea0ad34a1167a04490d763ed201bc4e254 Mon Sep 17 00:00:00 2001 From: Michal-Babins Date: Fri, 18 Oct 2024 18:48:01 +0000 Subject: [PATCH 2/3] updated md5 for merlin magic --- tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml | 2 +- tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml index cb21eb7ba..86f1a5a78 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: 8ab95440118d06dd3c07765a19e876e7 + md5sum: 82d53454e21c8e770e1db939aa1f2c77 - 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 e4076ec77..d97b832df 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: 8ab95440118d06dd3c07765a19e876e7 + md5sum: 82d53454e21c8e770e1db939aa1f2c77 - path: miniwdl_run/wdl/workflows/utilities/wf_read_QC_trim_se.wdl md5sum: d11bfe33fdd96eab28892be5a01c1c7d - path: miniwdl_run/workflow.log From a1774798ef1e68e868e3a837335d2ef2b8dabba0 Mon Sep 17 00:00:00 2001 From: Michal-Babins Date: Mon, 21 Oct 2024 19:29:12 +0000 Subject: [PATCH 3/3] updates to md5 sum --- tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml | 2 +- tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml index 86f1a5a78..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: 82d53454e21c8e770e1db939aa1f2c77 + 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 d97b832df..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: 82d53454e21c8e770e1db939aa1f2c77 + md5sum: 670f990128063eb3c7b3fa49302f08b7 - path: miniwdl_run/wdl/workflows/utilities/wf_read_QC_trim_se.wdl md5sum: d11bfe33fdd96eab28892be5a01c1c7d - path: miniwdl_run/workflow.log