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[MerlinMagic] Fixed output for crypto snippy_variants_num_variants #654

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merged 4 commits into from
Oct 22, 2024
Merged

[MerlinMagic] Fixed output for crypto snippy_variants_num_variants #654

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1f82443
fix num variants output for crypto
Michal-Babins Oct 18, 2024
ffd63fe
updated md5 for merlin magic
Michal-Babins Oct 18, 2024
334b4dd
Merge branch 'main' into mb-crypto-output-fix
sage-wright Oct 21, 2024
a177479
updates to md5 sum
Michal-Babins Oct 21, 2024
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2 changes: 1 addition & 1 deletion tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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2 changes: 1 addition & 1 deletion tests/workflows/theiaprok/test_wf_theiaprok_illumina_se.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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2 changes: 1 addition & 1 deletion workflows/utilities/wf_merlin_magic.wdl
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Expand Up @@ -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"])
}
}