From 4f8d071f62c6b14d5685ca6f6a5e2f59f339b7c6 Mon Sep 17 00:00:00 2001 From: William Rowell Date: Mon, 9 Dec 2024 12:44:56 -0800 Subject: [PATCH 01/22] Support for BAMs that lack basemods. --- docs/family.md | 18 ++++++++--------- docs/singleton.md | 18 ++++++++--------- wdl-ci.config.json | 30 +++++++++++++++++++++++++++++ workflows/downstream/downstream.wdl | 18 ++++++++--------- workflows/family.wdl | 18 ++++++++--------- workflows/singleton.wdl | 18 ++++++++--------- workflows/wdl-common | 2 +- 7 files changed, 76 insertions(+), 46 deletions(-) diff --git a/docs/family.md b/docs/family.md index 273f9e84..d334c9ad 100644 --- a/docs/family.md +++ b/docs/family.md @@ -223,15 +223,15 @@ The `Sample` struct contains sample specific data and metadata. The struct has t | Type | Name | Description | Notes | | ---- | ---- | ----------- | ----- | -| Array\[File\] | cpg_hap1_bed | CpG hap1 BED | | -| Array\[File\] | cpg_hap1_bed_index | | | -| Array\[File\] | cpg_hap2_bed | CpG hap2 BED | | -| Array\[File\] | cpg_hap2_bed_index | | | -| Array\[File\] | cpg_combined_bed | CpG combined BED | | -| Array\[File\] | cpg_combined_bed_index | | | -| Array\[File\] | cpg_hap1_bw | CpG hap1 BigWig | | -| Array\[File\] | cpg_hap2_bw | CpG hap2 BigWig | | -| Array\[File\] | cpg_combined_bw | CpG combined BigWig | | +| Array\[File?\] | cpg_hap1_bed | CpG hap1 BED | | +| Array\[File?\] | cpg_hap1_bed_index | | | +| Array\[File?\] | cpg_hap2_bed | CpG hap2 BED | | +| Array\[File?\] | cpg_hap2_bed_index | | | +| Array\[File?\] | cpg_combined_bed | CpG combined BED | | +| Array\[File?\] | cpg_combined_bed_index | | | +| Array\[File?\] | cpg_hap1_bw | CpG hap1 BigWig | | +| Array\[File?\] | cpg_hap2_bw | CpG hap2 BigWig | | +| Array\[File?\] | cpg_combined_bw | CpG combined BigWig | | | Array\[String\] | stat_cpg_hap1_count | Hap1 CpG count | | | Array\[String\] | stat_cpg_hap2_count | Hap2 CpG count | | | Array\[String\] | stat_cpg_combined_count | Combined CpG count | | diff --git a/docs/singleton.md b/docs/singleton.md index 6878ff97..7f571fc0 100644 --- a/docs/singleton.md +++ b/docs/singleton.md @@ -182,15 +182,15 @@ flowchart TD | Type | Name | Description | Notes | | ---- | ---- | ----------- | ----- | -| File | cpg_hap1_bed | CpG hap1 BED | | -| File | cpg_hap1_bed_index | | | -| File | cpg_hap2_bed | CpG hap2 BED | | -| File | cpg_hap2_bed_index | | | -| File | cpg_combined_bed | CpG combined BED | | -| File | cpg_combined_bed_index | | | -| File | cpg_hap1_bw | CpG hap1 BigWig | | -| File | cpg_hap2_bw | CpG hap2 BigWig | | -| File | cpg_combined_bw | CpG combined BigWig | | +| File? | cpg_hap1_bed | CpG hap1 BED | | +| File? | cpg_hap1_bed_index | | | +| File? | cpg_hap2_bed | CpG hap2 BED | | +| File? | cpg_hap2_bed_index | | | +| File? | cpg_combined_bed | CpG combined BED | | +| File? | cpg_combined_bed_index | | | +| File? | cpg_hap1_bw | CpG hap1 BigWig | | +| File? | cpg_hap2_bw | CpG hap2 BigWig | | +| File? | cpg_combined_bw | CpG combined BigWig | | | String | stat_cpg_hap1_count | Hap1 CpG count | | | String | stat_cpg_hap2_count | Hap2 CpG count | | | String | stat_cpg_combined_count | Combined CpG count | | diff --git a/wdl-ci.config.json b/wdl-ci.config.json index adc43376..91fd4d1d 100644 --- a/wdl-ci.config.json +++ b/wdl-ci.config.json @@ -665,6 +665,36 @@ ] } } + }, + { + "inputs": { + "haplotagged_bam": "${resources_file_path}/inputs/NA19238.GRCh38.chr6_10000000_20000000.haplotagged.bam", + "haplotagged_bam_index": "${resources_file_path}/inputs/NA19238.GRCh38.chr6_10000000_20000000.haplotagged.bam.bai", + "out_prefix": "NA19238.GRCh38", + "ref_fasta": "${ref_fasta}", + "ref_index": "${ref_index}", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "stat_hap1_cpg_count": { + "value": "0", + "test_tasks": [ + "compare_string" + ] + }, + "stat_hap2_cpg_count": { + "value": "0", + "test_tasks": [ + "compare_string" + ] + }, + "stat_combined_cpg_count": { + "value": "0", + "test_tasks": [ + "compare_string" + ] + } + } } ] } diff --git a/workflows/downstream/downstream.wdl b/workflows/downstream/downstream.wdl index 031ca870..70b6aeb4 100644 --- a/workflows/downstream/downstream.wdl +++ b/workflows/downstream/downstream.wdl @@ -198,15 +198,15 @@ workflow downstream { String stat_sv_BND_count = sv_stats.stat_sv_BND_count # cpg_pileup outputs - File cpg_combined_bed = cpg_pileup.combined_bed - File cpg_combined_bed_index = cpg_pileup.combined_bed_index - File cpg_hap1_bed = cpg_pileup.hap1_bed - File cpg_hap1_bed_index = cpg_pileup.hap1_bed_index - File cpg_hap2_bed = cpg_pileup.hap2_bed - File cpg_hap2_bed_index = cpg_pileup.hap2_bed_index - File cpg_combined_bw = cpg_pileup.combined_bw - File cpg_hap1_bw = cpg_pileup.hap1_bw - File cpg_hap2_bw = cpg_pileup.hap2_bw + File? cpg_combined_bed = cpg_pileup.combined_bed + File? cpg_combined_bed_index = cpg_pileup.combined_bed_index + File? cpg_hap1_bed = cpg_pileup.hap1_bed + File? cpg_hap1_bed_index = cpg_pileup.hap1_bed_index + File? cpg_hap2_bed = cpg_pileup.hap2_bed + File? cpg_hap2_bed_index = cpg_pileup.hap2_bed_index + File? cpg_combined_bw = cpg_pileup.combined_bw + File? cpg_hap1_bw = cpg_pileup.hap1_bw + File? cpg_hap2_bw = cpg_pileup.hap2_bw String stat_hap1_cpg_count = cpg_pileup.stat_hap1_cpg_count String stat_hap2_cpg_count = cpg_pileup.stat_hap2_cpg_count String stat_combined_cpg_count = cpg_pileup.stat_combined_cpg_count diff --git a/workflows/family.wdl b/workflows/family.wdl index 7c86be9d..7fb3ef0a 100644 --- a/workflows/family.wdl +++ b/workflows/family.wdl @@ -304,15 +304,15 @@ workflow humanwgs_family { Array[String] stat_phase_block_ng50 = downstream.stat_phase_block_ng50 # cpg_pileup outputs - Array[File] cpg_combined_bed = downstream.cpg_combined_bed - Array[File] cpg_combined_bed_index = downstream.cpg_combined_bed_index - Array[File] cpg_hap1_bed = downstream.cpg_hap1_bed - Array[File] cpg_hap1_bed_index = downstream.cpg_hap1_bed_index - Array[File] cpg_hap2_bed = downstream.cpg_hap2_bed - Array[File] cpg_hap2_bed_index = downstream.cpg_hap2_bed_index - Array[File] cpg_combined_bw = downstream.cpg_combined_bw - Array[File] cpg_hap1_bw = downstream.cpg_hap1_bw - Array[File] cpg_hap2_bw = downstream.cpg_hap2_bw + Array[File?] cpg_combined_bed = downstream.cpg_combined_bed + Array[File?] cpg_combined_bed_index = downstream.cpg_combined_bed_index + Array[File?] cpg_hap1_bed = downstream.cpg_hap1_bed + Array[File?] cpg_hap1_bed_index = downstream.cpg_hap1_bed_index + Array[File?] cpg_hap2_bed = downstream.cpg_hap2_bed + Array[File?] cpg_hap2_bed_index = downstream.cpg_hap2_bed_index + Array[File?] cpg_combined_bw = downstream.cpg_combined_bw + Array[File?] cpg_hap1_bw = downstream.cpg_hap1_bw + Array[File?] cpg_hap2_bw = downstream.cpg_hap2_bw Array[String] stat_cpg_hap1_count = downstream.stat_hap1_cpg_count Array[String] stat_cpg_hap2_count = downstream.stat_hap2_cpg_count Array[String] stat_cpg_combined_count = downstream.stat_combined_cpg_count diff --git a/workflows/singleton.wdl b/workflows/singleton.wdl index ae3cdb83..170b8ff5 100644 --- a/workflows/singleton.wdl +++ b/workflows/singleton.wdl @@ -244,15 +244,15 @@ workflow humanwgs_singleton { String stat_phase_block_ng50 = downstream.stat_phase_block_ng50 # cpg_pileup outputs - File cpg_combined_bed = downstream.cpg_combined_bed - File cpg_combined_bed_index = downstream.cpg_combined_bed_index - File cpg_hap1_bed = downstream.cpg_hap1_bed - File cpg_hap1_bed_index = downstream.cpg_hap1_bed_index - File cpg_hap2_bed = downstream.cpg_hap2_bed - File cpg_hap2_bed_index = downstream.cpg_hap2_bed_index - File cpg_combined_bw = downstream.cpg_combined_bw - File cpg_hap1_bw = downstream.cpg_hap1_bw - File cpg_hap2_bw = downstream.cpg_hap2_bw + File? cpg_combined_bed = downstream.cpg_combined_bed + File? cpg_combined_bed_index = downstream.cpg_combined_bed_index + File? cpg_hap1_bed = downstream.cpg_hap1_bed + File? cpg_hap1_bed_index = downstream.cpg_hap1_bed_index + File? cpg_hap2_bed = downstream.cpg_hap2_bed + File? cpg_hap2_bed_index = downstream.cpg_hap2_bed_index + File? cpg_combined_bw = downstream.cpg_combined_bw + File? cpg_hap1_bw = downstream.cpg_hap1_bw + File? cpg_hap2_bw = downstream.cpg_hap2_bw String stat_cpg_hap1_count = downstream.stat_hap1_cpg_count String stat_cpg_hap2_count = downstream.stat_hap2_cpg_count String stat_cpg_combined_count = downstream.stat_combined_cpg_count diff --git a/workflows/wdl-common b/workflows/wdl-common index 60e9eb5c..89245658 160000 --- a/workflows/wdl-common +++ b/workflows/wdl-common @@ -1 +1 @@ -Subproject commit 60e9eb5c798b6d35dc26fe8561423cf1dab193bd +Subproject commit 892456583b4e9f17761bd2ff0585f45d01609ce1 From 85472e840fdadd6b630ddf3c4b4f1d80d3606cd4 Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Mon, 9 Dec 2024 23:16:14 +0000 Subject: [PATCH 02/22] update wdl-ci config file after successful tests --- wdl-ci.config.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wdl-ci.config.json b/wdl-ci.config.json index 91fd4d1d..25043b8f 100644 --- a/wdl-ci.config.json +++ b/wdl-ci.config.json @@ -586,7 +586,7 @@ "tasks": { "cpg_pileup": { "key": "cpg_pileup", - "digest": "noq7e5yf5h6s2sf7lzolbgigqec4izmg", + "digest": "km7kr546iovkhccy3yb2ovvvdmmnmet7", "tests": [ { "inputs": { From 342d25945de20a749c2633bf60f11c37702e7cd2 Mon Sep 17 00:00:00 2001 From: William Rowell Date: Mon, 9 Dec 2024 15:31:19 -0800 Subject: [PATCH 03/22] Support input without rq values. --- docs/family.md | 2 +- docs/singleton.md | 2 +- wdl-ci.config.json | 28 ++++++++++++++++++++++++++++ workflows/family.wdl | 2 +- workflows/singleton.wdl | 2 +- workflows/upstream/upstream.wdl | 2 +- workflows/wdl-common | 2 +- 7 files changed, 34 insertions(+), 6 deletions(-) diff --git a/docs/family.md b/docs/family.md index d334c9ad..ed7fa7c2 100644 --- a/docs/family.md +++ b/docs/family.md @@ -119,7 +119,7 @@ The `Sample` struct contains sample specific data and metadata. The struct has t | File | stats_file | Table of summary statistics | | | Array\[File\] | bam_stats | BAM stats | Per-read length and read-quality | | Array\[File\] | read_length_plot | Read length plot | | -| Array\[File\] | read_quality_plot | Read quality plot | | +| Array\[File?\] | read_quality_plot | Read quality plot | | | Array\[File\] | merged_haplotagged_bam | Merged, haplotagged alignments | Includes unmapped reads | | Array\[File\] | merged_haplotagged_bam_index | | | | Array\[File\] | mosdepth_summary | Summary of aligned read depth. | | diff --git a/docs/singleton.md b/docs/singleton.md index 7f571fc0..38c0bfe7 100644 --- a/docs/singleton.md +++ b/docs/singleton.md @@ -84,7 +84,7 @@ flowchart TD | File | stats_file | Table of summary statistics | | | File | bam_stats | BAM stats | Per-read length and read-quality | | File | read_length_plot | Read length plot | | -| File | read_quality_plot | Read quality plot | | +| File? | read_quality_plot | Read quality plot | | | File | merged_haplotagged_bam | Merged, haplotagged alignments | Includes unmapped reads | | File | merged_haplotagged_bam_index | | | | File | mosdepth_summary | Summary of aligned read depth. | | diff --git a/wdl-ci.config.json b/wdl-ci.config.json index 25043b8f..353237e5 100644 --- a/wdl-ci.config.json +++ b/wdl-ci.config.json @@ -1382,6 +1382,34 @@ ] } } + }, + { + "inputs": { + "sample_id": "HG002", + "bam": "${resources_file_path}/inputs/vega_10k.no_rq.hifi_reads.bam", + "ref_fasta": "${ref_fasta}", + "ref_index": "${ref_index}", + "ref_name": "${ref_name}", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "aligned_bam": { + "value": "${resources_file_path}/pbmm2_align_wgs/vega_10k_no_rq/HG002.vega_10k.no_rq.hifi_reads.GRCh38.aligned.bam", + "test_tasks": [ + "compare_file_basename", + "samtools_quickcheck" + ] + }, + "bam_stats": { + "value": "${resources_file_path}/pbmm2_align_wgs/vega_10k_no_rq/HG002.vega_10k.no_rq.hifi_reads.read_length_and_quality.tsv.gz", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_columns", + "check_gzip" + ] + } + } } ] } diff --git a/workflows/family.wdl b/workflows/family.wdl index 7fb3ef0a..bfe9cec5 100644 --- a/workflows/family.wdl +++ b/workflows/family.wdl @@ -273,7 +273,7 @@ workflow humanwgs_family { # bam stats Array[File] bam_stats = upstream.read_length_and_quality Array[File] read_length_plot = upstream.read_length_plot - Array[File] read_quality_plot = upstream.read_quality_plot + Array[File?] read_quality_plot = upstream.read_quality_plot Array[String] stat_num_reads = upstream.stat_num_reads Array[String] stat_read_length_mean = upstream.stat_read_length_mean Array[String] stat_read_length_median = upstream.stat_read_length_median diff --git a/workflows/singleton.wdl b/workflows/singleton.wdl index 170b8ff5..ef7008df 100644 --- a/workflows/singleton.wdl +++ b/workflows/singleton.wdl @@ -213,7 +213,7 @@ workflow humanwgs_singleton { # bam stats File bam_stats = upstream.read_length_and_quality File read_length_plot = upstream.read_length_plot - File read_quality_plot = upstream.read_quality_plot + File? read_quality_plot = upstream.read_quality_plot String stat_num_reads = upstream.stat_num_reads String stat_read_length_mean = upstream.stat_read_length_mean String stat_read_length_median = upstream.stat_read_length_median diff --git a/workflows/upstream/upstream.wdl b/workflows/upstream/upstream.wdl index 93635376..05639dd8 100644 --- a/workflows/upstream/upstream.wdl +++ b/workflows/upstream/upstream.wdl @@ -219,7 +219,7 @@ workflow upstream { # bam stats File read_length_and_quality = merge_bam_stats.read_length_and_quality File read_length_plot = merge_bam_stats.read_length_plot - File read_quality_plot = merge_bam_stats.read_quality_plot + File? read_quality_plot = merge_bam_stats.read_quality_plot String stat_num_reads = merge_bam_stats.stat_num_reads String stat_read_length_mean = merge_bam_stats.stat_read_length_mean String stat_read_length_median = merge_bam_stats.stat_read_length_median diff --git a/workflows/wdl-common b/workflows/wdl-common index 89245658..43d68579 160000 --- a/workflows/wdl-common +++ b/workflows/wdl-common @@ -1 +1 @@ -Subproject commit 892456583b4e9f17761bd2ff0585f45d01609ce1 +Subproject commit 43d68579cd241c19d5ae8a581e7e71fe289347a4 From 8445aedf61746d0b30731b7ad0d183ff4577cabd Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue, 10 Dec 2024 01:57:32 +0000 Subject: [PATCH 04/22] update wdl-ci config file after successful tests --- wdl-ci.config.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/wdl-ci.config.json b/wdl-ci.config.json index 353237e5..ad39e6df 100644 --- a/wdl-ci.config.json +++ b/wdl-ci.config.json @@ -964,7 +964,7 @@ "tasks": { "merge_bam_stats": { "key": "merge_bam_stats", - "digest": "k2zoxoqmson4rr7meogbb675w3bnj2gt", + "digest": "fgbffrsqd32kov6i43cidmt2u5lgvn7g", "tests": [ { "inputs": { @@ -1268,7 +1268,7 @@ "tasks": { "pbmm2_align_wgs": { "key": "pbmm2_align_wgs", - "digest": "r2mrlrcc34hmpeetxabc7ujwfb2zzykq", + "digest": "jnyotwps3swl7ulnqunr5ktstoxdbvs3", "tests": [ { "inputs": { From ecdbf3e2703bc2073c61b9fe586b2a3c2380974a Mon Sep 17 00:00:00 2001 From: William Rowell Date: Mon, 9 Dec 2024 18:00:25 -0800 Subject: [PATCH 05/22] Added merge_bam_stats test for sample with no rq. --- wdl-ci.config.json | 58 ++++++++++++++++++++++++++++++++++++++++++++ workflows/wdl-common | 2 +- 2 files changed, 59 insertions(+), 1 deletion(-) diff --git a/wdl-ci.config.json b/wdl-ci.config.json index ad39e6df..590ad855 100644 --- a/wdl-ci.config.json +++ b/wdl-ci.config.json @@ -1098,6 +1098,64 @@ ] } } + }, + { + "inputs": { + "sample_id": "HG002", + "bam_stats": [ + "${resources_file_path}/pbmm2_align_wgs/vega_10k_no_rq/HG002.vega_10k.no_rq.hifi_reads.read_length_and_quality.tsv.gz" + ], + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "read_length_and_quality": { + "value": "${resources_file_path}/merge_bam_stats/no_rq/HG002.read_length_and_quality.tsv.gz", + "test_tasks": [ + "compare_file_basename", + "check_tab_delimited", + "count_columns", + "check_gzip" + ] + }, + "read_length_plot": { + "value": "${resources_file_path}/merge_bam_stats/no_rq/HG002.read_length_histogram.png", + "test_tasks": [ + "calculate_md5sum", + "compare_file_basename", + "png_validator" + ] + }, + "stat_num_reads": { + "value": "10000", + "test_tasks": [ + "compare_string" + ] + }, + "stat_read_length_mean": { + "value": "21837.4", + "test_tasks": [ + "compare_string" + ] + }, + "stat_read_length_median": { + "value": "21385.0", + "test_tasks": [ + "compare_string" + ] + }, + "stat_read_quality_mean": { + "value": "nan", + "test_tasks": [ + "compare_string" + ] + }, + "stat_read_quality_median": { + "value": "nan", + "test_tasks": [ + "compare_string" + ] + } + } } ] } diff --git a/workflows/wdl-common b/workflows/wdl-common index 43d68579..4ca54791 160000 --- a/workflows/wdl-common +++ b/workflows/wdl-common @@ -1 +1 @@ -Subproject commit 43d68579cd241c19d5ae8a581e7e71fe289347a4 +Subproject commit 4ca54791d3f8fabd88872df3cd8ec81ed8a516c6 From 381313bcaa452c550209dd6a78dd0eb803d4b969 Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue, 10 Dec 2024 02:34:25 +0000 Subject: [PATCH 06/22] update wdl-ci config file after successful tests --- wdl-ci.config.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wdl-ci.config.json b/wdl-ci.config.json index 590ad855..cec8daa3 100644 --- a/wdl-ci.config.json +++ b/wdl-ci.config.json @@ -964,7 +964,7 @@ "tasks": { "merge_bam_stats": { "key": "merge_bam_stats", - "digest": "fgbffrsqd32kov6i43cidmt2u5lgvn7g", + "digest": "mjd6zpbxtabbulmq3kwhcx4cnubxaf74", "tests": [ { "inputs": { From 71a1115d9b0c1c6ab320d36468506d1ddd633bb6 Mon Sep 17 00:00:00 2001 From: William Rowell Date: Wed, 27 Nov 2024 10:01:20 -0800 Subject: [PATCH 07/22] Updated to TRGT v1.4.1. - changed trgt `samtools sort` to use 8 threads to address OOM --- wdl-ci.config.json | 4 ++-- workflows/wdl-common | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/wdl-ci.config.json b/wdl-ci.config.json index cec8daa3..c8802f9f 100644 --- a/wdl-ci.config.json +++ b/wdl-ci.config.json @@ -1678,7 +1678,7 @@ "tasks": { "trgt": { "key": "trgt", - "digest": "rpcfzfr5reqxv7jbtfncu6etivzxvgs2", + "digest": "6i7troewkutvnmy6oft2vkgeltp2jh3z", "tests": [ { "inputs": { @@ -1767,7 +1767,7 @@ }, "trgt_merge": { "key": "trgt_merge", - "digest": "cmdcqkqrcfpn2eoczxfwhs6zqhalzdtt", + "digest": "ljvpgmkt7sfdwpm64dqllrphd23ols56", "tests": [ { "inputs": { diff --git a/workflows/wdl-common b/workflows/wdl-common index 4ca54791..644a3153 160000 --- a/workflows/wdl-common +++ b/workflows/wdl-common @@ -1 +1 @@ -Subproject commit 4ca54791d3f8fabd88872df3cd8ec81ed8a516c6 +Subproject commit 644a3153462e572298c7b737c7011830007b5599 From a0504ae144aa3fd7d3912d13d4842464886bee43 Mon Sep 17 00:00:00 2001 From: William Rowell Date: Thu, 12 Dec 2024 18:18:44 -0800 Subject: [PATCH 08/22] Address trgt OOM errors when using catalogs with very low complexity sites. --- workflows/wdl-common | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/wdl-common b/workflows/wdl-common index 644a3153..8901fdfb 160000 --- a/workflows/wdl-common +++ b/workflows/wdl-common @@ -1 +1 @@ -Subproject commit 644a3153462e572298c7b737c7011830007b5599 +Subproject commit 8901fdfbe5cfb53938d2fe099f022146b82e043f From b7934ed73bd633b7997348f3d8f37e59154a8ba8 Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Tue, 17 Dec 2024 23:26:18 +0000 Subject: [PATCH 09/22] update wdl-ci config file after successful tests --- wdl-ci.config.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wdl-ci.config.json b/wdl-ci.config.json index c8802f9f..4319efae 100644 --- a/wdl-ci.config.json +++ b/wdl-ci.config.json @@ -1678,7 +1678,7 @@ "tasks": { "trgt": { "key": "trgt", - "digest": "6i7troewkutvnmy6oft2vkgeltp2jh3z", + "digest": "37d5grkookrgta6rwpmlrce3zkjavpmy", "tests": [ { "inputs": { From 108657f5c2a9d35c2d25eb0d95ab93c7456ccddd Mon Sep 17 00:00:00 2001 From: William Rowell Date: Tue, 17 Dec 2024 17:34:25 -0800 Subject: [PATCH 10/22] Update to pbmm2 v1.16.99 prerelease. Release fixes behavior where `SA` tags were not stripped from aligned input. --- workflows/wdl-common | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/wdl-common b/workflows/wdl-common index 8901fdfb..19be8c7a 160000 --- a/workflows/wdl-common +++ b/workflows/wdl-common @@ -1 +1 @@ -Subproject commit 8901fdfbe5cfb53938d2fe099f022146b82e043f +Subproject commit 19be8c7a02edc77c42fff38cd7fdd6775689c373 From d95939945c43eaf9cf7d93f70519a11eac924b14 Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 18 Dec 2024 01:56:09 +0000 Subject: [PATCH 11/22] update wdl-ci config file after successful tests --- wdl-ci.config.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wdl-ci.config.json b/wdl-ci.config.json index 4319efae..8c7c4360 100644 --- a/wdl-ci.config.json +++ b/wdl-ci.config.json @@ -1326,7 +1326,7 @@ "tasks": { "pbmm2_align_wgs": { "key": "pbmm2_align_wgs", - "digest": "jnyotwps3swl7ulnqunr5ktstoxdbvs3", + "digest": "lfkj5u6d6hakjxcmp3q6nzpwuz3jz5l3", "tests": [ { "inputs": { From a6a0565a2b231c5c9c284ddc628a6b924a21dc06 Mon Sep 17 00:00:00 2001 From: William Rowell Date: Tue, 17 Dec 2024 16:26:37 -0800 Subject: [PATCH 12/22] Filter `NO_READS` no-call lines from StarPhase input to PharmCAT. --- workflows/wdl-common | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/wdl-common b/workflows/wdl-common index 19be8c7a..99b463b8 160000 --- a/workflows/wdl-common +++ b/workflows/wdl-common @@ -1 +1 @@ -Subproject commit 19be8c7a02edc77c42fff38cd7fdd6775689c373 +Subproject commit 99b463b8427f1158916705705fbdc998392c06be From 0e6292a1b3ed2ff5e7058f30021198e7ff9bc8a5 Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 18 Dec 2024 00:33:18 +0000 Subject: [PATCH 13/22] update wdl-ci config file after successful tests --- wdl-ci.config.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wdl-ci.config.json b/wdl-ci.config.json index 8c7c4360..1c41e9f9 100644 --- a/wdl-ci.config.json +++ b/wdl-ci.config.json @@ -2415,7 +2415,7 @@ }, "run_pharmcat": { "key": "run_pharmcat", - "digest": "bpvbkvx6hsvzy7a3mymzjrwqvgxdrmj7", + "digest": "uknkltw6uwppbf5ttzrsifayz4pqplvi", "tests": [ { "inputs": { From 21ab0ef650017e04c5d74a8e370cc1cafd840adf Mon Sep 17 00:00:00 2001 From: William Rowell Date: Tue, 17 Dec 2024 16:50:27 -0800 Subject: [PATCH 14/22] Only attempt to run PharmCAT if at least one PharmCAT region has depth > pharmcat_min_coverage - make PharmCAT outputs optional --- workflows/downstream/downstream.wdl | 26 +++---- workflows/family.wdl | 110 ++++++++++++++-------------- workflows/singleton.wdl | 28 +++---- 3 files changed, 82 insertions(+), 82 deletions(-) diff --git a/workflows/downstream/downstream.wdl b/workflows/downstream/downstream.wdl index 70b6aeb4..2f509fc9 100644 --- a/workflows/downstream/downstream.wdl +++ b/workflows/downstream/downstream.wdl @@ -198,15 +198,15 @@ workflow downstream { String stat_sv_BND_count = sv_stats.stat_sv_BND_count # cpg_pileup outputs - File? cpg_combined_bed = cpg_pileup.combined_bed - File? cpg_combined_bed_index = cpg_pileup.combined_bed_index - File? cpg_hap1_bed = cpg_pileup.hap1_bed - File? cpg_hap1_bed_index = cpg_pileup.hap1_bed_index - File? cpg_hap2_bed = cpg_pileup.hap2_bed - File? cpg_hap2_bed_index = cpg_pileup.hap2_bed_index - File? cpg_combined_bw = cpg_pileup.combined_bw - File? cpg_hap1_bw = cpg_pileup.hap1_bw - File? cpg_hap2_bw = cpg_pileup.hap2_bw + File? cpg_combined_bed = cpg_pileup.combined_bed + File? cpg_combined_bed_index = cpg_pileup.combined_bed_index + File? cpg_hap1_bed = cpg_pileup.hap1_bed + File? cpg_hap1_bed_index = cpg_pileup.hap1_bed_index + File? cpg_hap2_bed = cpg_pileup.hap2_bed + File? cpg_hap2_bed_index = cpg_pileup.hap2_bed_index + File? cpg_combined_bw = cpg_pileup.combined_bw + File? cpg_hap1_bw = cpg_pileup.hap1_bw + File? cpg_hap2_bw = cpg_pileup.hap2_bw String stat_hap1_cpg_count = cpg_pileup.stat_hap1_cpg_count String stat_hap2_cpg_count = cpg_pileup.stat_hap2_cpg_count String stat_combined_cpg_count = cpg_pileup.stat_combined_cpg_count @@ -215,9 +215,9 @@ workflow downstream { File pbstarphase_json = pbstarphase_diplotype.out_json # pharmcat and pangu outputs - File pharmcat_match_json = pharmcat.pharmcat_match_json - File pharmcat_phenotype_json = pharmcat.pharmcat_phenotype_json - File pharmcat_report_html = pharmcat.pharmcat_report_html - File pharmcat_report_json = pharmcat.pharmcat_report_json + File? pharmcat_match_json = pharmcat.pharmcat_match_json + File? pharmcat_phenotype_json = pharmcat.pharmcat_phenotype_json + File? pharmcat_report_html = pharmcat.pharmcat_report_html + File? pharmcat_report_json = pharmcat.pharmcat_report_json } } \ No newline at end of file diff --git a/workflows/family.wdl b/workflows/family.wdl index bfe9cec5..33ac817b 100644 --- a/workflows/family.wdl +++ b/workflows/family.wdl @@ -271,9 +271,9 @@ workflow humanwgs_family { File stats_file = consolidate_stats.output_tsv # bam stats - Array[File] bam_stats = upstream.read_length_and_quality - Array[File] read_length_plot = upstream.read_length_plot - Array[File?] read_quality_plot = upstream.read_quality_plot + Array[File] bam_stats = upstream.read_length_and_quality + Array[File] read_length_plot = upstream.read_length_plot + Array[File?] read_quality_plot = upstream.read_quality_plot Array[String] stat_num_reads = upstream.stat_num_reads Array[String] stat_read_length_mean = upstream.stat_read_length_mean Array[String] stat_read_length_median = upstream.stat_read_length_median @@ -281,38 +281,38 @@ workflow humanwgs_family { Array[String] stat_read_quality_median = upstream.stat_read_quality_median # merged, haplotagged alignments - Array[File] merged_haplotagged_bam = downstream.merged_haplotagged_bam - Array[File] merged_haplotagged_bam_index = downstream.merged_haplotagged_bam_index - Array[String] stat_mapped_read_count = downstream.stat_mapped_read_count - Array[String] stat_mapped_percent = downstream.stat_mapped_percent - Array[File] mapq_distribution_plot = downstream.mapq_distribution_plot - Array[File] mg_distribution_plot = downstream.mg_distribution_plot + Array[File] merged_haplotagged_bam = downstream.merged_haplotagged_bam + Array[File] merged_haplotagged_bam_index = downstream.merged_haplotagged_bam_index + Array[String] stat_mapped_read_count = downstream.stat_mapped_read_count + Array[String] stat_mapped_percent = downstream.stat_mapped_percent + Array[File] mapq_distribution_plot = downstream.mapq_distribution_plot + Array[File] mg_distribution_plot = downstream.mg_distribution_plot # mosdepth outputs - Array[File] mosdepth_summary = upstream.mosdepth_summary - Array[File] mosdepth_region_bed = upstream.mosdepth_region_bed - Array[File] mosdepth_region_bed_index = upstream.mosdepth_region_bed_index - Array[File] mosdepth_depth_distribution_plot = upstream.mosdepth_depth_distribution_plot - Array[String] stat_mean_depth = upstream.stat_mean_depth - Array[String] inferred_sex = upstream.inferred_sex + Array[File] mosdepth_summary = upstream.mosdepth_summary + Array[File] mosdepth_region_bed = upstream.mosdepth_region_bed + Array[File] mosdepth_region_bed_index = upstream.mosdepth_region_bed_index + Array[File] mosdepth_depth_distribution_plot = upstream.mosdepth_depth_distribution_plot + Array[String] stat_mean_depth = upstream.stat_mean_depth + Array[String] inferred_sex = upstream.inferred_sex # phasing stats - Array[File] phase_stats = downstream.phase_stats - Array[File] phase_blocks = downstream.phase_blocks - Array[File] phase_haplotags = downstream.phase_haplotags + Array[File] phase_stats = downstream.phase_stats + Array[File] phase_blocks = downstream.phase_blocks + Array[File] phase_haplotags = downstream.phase_haplotags Array[String] stat_phased_basepairs = downstream.stat_phased_basepairs Array[String] stat_phase_block_ng50 = downstream.stat_phase_block_ng50 # cpg_pileup outputs - Array[File?] cpg_combined_bed = downstream.cpg_combined_bed - Array[File?] cpg_combined_bed_index = downstream.cpg_combined_bed_index - Array[File?] cpg_hap1_bed = downstream.cpg_hap1_bed - Array[File?] cpg_hap1_bed_index = downstream.cpg_hap1_bed_index - Array[File?] cpg_hap2_bed = downstream.cpg_hap2_bed - Array[File?] cpg_hap2_bed_index = downstream.cpg_hap2_bed_index - Array[File?] cpg_combined_bw = downstream.cpg_combined_bw - Array[File?] cpg_hap1_bw = downstream.cpg_hap1_bw - Array[File?] cpg_hap2_bw = downstream.cpg_hap2_bw + Array[File?] cpg_combined_bed = downstream.cpg_combined_bed + Array[File?] cpg_combined_bed_index = downstream.cpg_combined_bed_index + Array[File?] cpg_hap1_bed = downstream.cpg_hap1_bed + Array[File?] cpg_hap1_bed_index = downstream.cpg_hap1_bed_index + Array[File?] cpg_hap2_bed = downstream.cpg_hap2_bed + Array[File?] cpg_hap2_bed_index = downstream.cpg_hap2_bed_index + Array[File?] cpg_combined_bw = downstream.cpg_combined_bw + Array[File?] cpg_hap1_bw = downstream.cpg_hap1_bw + Array[File?] cpg_hap2_bw = downstream.cpg_hap2_bw Array[String] stat_cpg_hap1_count = downstream.stat_hap1_cpg_count Array[String] stat_cpg_hap2_count = downstream.stat_hap2_cpg_count Array[String] stat_cpg_combined_count = downstream.stat_combined_cpg_count @@ -335,48 +335,48 @@ workflow humanwgs_family { Array[File] small_variant_gvcf_index = upstream.small_variant_gvcf_index # small variant stats - Array[File] small_variant_stats = downstream.small_variant_stats - Array[File] bcftools_roh_out = downstream.bcftools_roh_out - Array[File] bcftools_roh_bed = downstream.bcftools_roh_bed + Array[File] small_variant_stats = downstream.small_variant_stats + Array[File] bcftools_roh_out = downstream.bcftools_roh_out + Array[File] bcftools_roh_bed = downstream.bcftools_roh_bed Array[String] stat_small_variant_SNV_count = downstream.stat_SNV_count Array[String] stat_small_variant_INDEL_count = downstream.stat_INDEL_count Array[String] stat_small_variant_TSTV_ratio = downstream.stat_TSTV_ratio Array[String] stat_small_variant_HETHOM_ratio = downstream.stat_HETHOM_ratio - Array[File] snv_distribution_plot = downstream.snv_distribution_plot - Array[File] indel_distribution_plot = downstream.indel_distribution_plot + Array[File] snv_distribution_plot = downstream.snv_distribution_plot + Array[File] indel_distribution_plot = downstream.indel_distribution_plot # trgt outputs - Array[File] phased_trgt_vcf = downstream.phased_trgt_vcf - Array[File] phased_trgt_vcf_index = downstream.phased_trgt_vcf_index - Array[File] trgt_spanning_reads = upstream.trgt_spanning_reads - Array[File] trgt_spanning_reads_index = upstream.trgt_spanning_reads_index - Array[File] trgt_coverage_dropouts = upstream.trgt_coverage_dropouts + Array[File] phased_trgt_vcf = downstream.phased_trgt_vcf + Array[File] phased_trgt_vcf_index = downstream.phased_trgt_vcf_index + Array[File] trgt_spanning_reads = upstream.trgt_spanning_reads + Array[File] trgt_spanning_reads_index = upstream.trgt_spanning_reads_index + Array[File] trgt_coverage_dropouts = upstream.trgt_coverage_dropouts Array[String] stat_trgt_genotyped_count = upstream.stat_trgt_genotyped_count Array[String] stat_trgt_uncalled_count = upstream.stat_trgt_uncalled_count # paraphase outputs - Array[File] paraphase_output_json = upstream.paraphase_output_json - Array[File] paraphase_realigned_bam = upstream.paraphase_realigned_bam - Array[File] paraphase_realigned_bam_index = upstream.paraphase_realigned_bam_index - Array[File?] paraphase_vcfs = upstream.paraphase_vcfs + Array[File] paraphase_output_json = upstream.paraphase_output_json + Array[File] paraphase_realigned_bam = upstream.paraphase_realigned_bam + Array[File] paraphase_realigned_bam_index = upstream.paraphase_realigned_bam_index + Array[File?] paraphase_vcfs = upstream.paraphase_vcfs # per sample cnv outputs - Array[File] cnv_vcf = upstream.cnv_vcf - Array[File] cnv_vcf_index = upstream.cnv_vcf_index - Array[File] cnv_copynum_bedgraph = upstream.cnv_copynum_bedgraph - Array[File] cnv_depth_bw = upstream.cnv_depth_bw - Array[File] cnv_maf_bw = upstream.cnv_maf_bw - Array[String] stat_cnv_DUP_count = upstream.stat_cnv_DUP_count - Array[String] stat_cnv_DEL_count = upstream.stat_cnv_DEL_count - Array[String] stat_cnv_DUP_sum = upstream.stat_cnv_DUP_sum - Array[String] stat_cnv_DEL_sum = upstream.stat_cnv_DEL_sum + Array[File] cnv_vcf = upstream.cnv_vcf + Array[File] cnv_vcf_index = upstream.cnv_vcf_index + Array[File] cnv_copynum_bedgraph = upstream.cnv_copynum_bedgraph + Array[File] cnv_depth_bw = upstream.cnv_depth_bw + Array[File] cnv_maf_bw = upstream.cnv_maf_bw + Array[String] stat_cnv_DUP_count = upstream.stat_cnv_DUP_count + Array[String] stat_cnv_DEL_count = upstream.stat_cnv_DEL_count + Array[String] stat_cnv_DUP_sum = upstream.stat_cnv_DUP_sum + Array[String] stat_cnv_DEL_sum = upstream.stat_cnv_DEL_sum # PGx outputs - Array[File] pbstarphase_json = downstream.pbstarphase_json - Array[File] pharmcat_match_json = downstream.pharmcat_match_json - Array[File] pharmcat_phenotype_json = downstream.pharmcat_phenotype_json - Array[File] pharmcat_report_html = downstream.pharmcat_report_html - Array[File] pharmcat_report_json = downstream.pharmcat_report_json + Array[File] pbstarphase_json = downstream.pbstarphase_json + Array[File?] pharmcat_match_json = downstream.pharmcat_match_json + Array[File?] pharmcat_phenotype_json = downstream.pharmcat_phenotype_json + Array[File?] pharmcat_report_html = downstream.pharmcat_report_html + Array[File?] pharmcat_report_json = downstream.pharmcat_report_json # joint call outputs File? joint_small_variants_vcf = merge_small_variant_vcfs.merged_vcf diff --git a/workflows/singleton.wdl b/workflows/singleton.wdl index ef7008df..fde0a69e 100644 --- a/workflows/singleton.wdl +++ b/workflows/singleton.wdl @@ -244,15 +244,15 @@ workflow humanwgs_singleton { String stat_phase_block_ng50 = downstream.stat_phase_block_ng50 # cpg_pileup outputs - File? cpg_combined_bed = downstream.cpg_combined_bed - File? cpg_combined_bed_index = downstream.cpg_combined_bed_index - File? cpg_hap1_bed = downstream.cpg_hap1_bed - File? cpg_hap1_bed_index = downstream.cpg_hap1_bed_index - File? cpg_hap2_bed = downstream.cpg_hap2_bed - File? cpg_hap2_bed_index = downstream.cpg_hap2_bed_index - File? cpg_combined_bw = downstream.cpg_combined_bw - File? cpg_hap1_bw = downstream.cpg_hap1_bw - File? cpg_hap2_bw = downstream.cpg_hap2_bw + File? cpg_combined_bed = downstream.cpg_combined_bed + File? cpg_combined_bed_index = downstream.cpg_combined_bed_index + File? cpg_hap1_bed = downstream.cpg_hap1_bed + File? cpg_hap1_bed_index = downstream.cpg_hap1_bed_index + File? cpg_hap2_bed = downstream.cpg_hap2_bed + File? cpg_hap2_bed_index = downstream.cpg_hap2_bed_index + File? cpg_combined_bw = downstream.cpg_combined_bw + File? cpg_hap1_bw = downstream.cpg_hap1_bw + File? cpg_hap2_bw = downstream.cpg_hap2_bw String stat_cpg_hap1_count = downstream.stat_hap1_cpg_count String stat_cpg_hap2_count = downstream.stat_hap2_cpg_count String stat_cpg_combined_count = downstream.stat_combined_cpg_count @@ -312,11 +312,11 @@ workflow humanwgs_singleton { String stat_cnv_DEL_sum = upstream.stat_cnv_DEL_sum # PGx outputs - File pbstarphase_json = downstream.pbstarphase_json - File pharmcat_match_json = downstream.pharmcat_match_json - File pharmcat_phenotype_json = downstream.pharmcat_phenotype_json - File pharmcat_report_html = downstream.pharmcat_report_html - File pharmcat_report_json = downstream.pharmcat_report_json + File pbstarphase_json = downstream.pbstarphase_json + File? pharmcat_match_json = downstream.pharmcat_match_json + File? pharmcat_phenotype_json = downstream.pharmcat_phenotype_json + File? pharmcat_report_html = downstream.pharmcat_report_html + File? pharmcat_report_json = downstream.pharmcat_report_json # tertiary analysis outputs File? pedigree = write_ped_phrank.pedigree From d291a4d5d686be4eb5138b68ed280a26bf5ad11b Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 18 Dec 2024 00:55:44 +0000 Subject: [PATCH 15/22] update wdl-ci config file after successful tests --- wdl-ci.config.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wdl-ci.config.json b/wdl-ci.config.json index 1c41e9f9..134c417f 100644 --- a/wdl-ci.config.json +++ b/wdl-ci.config.json @@ -2390,7 +2390,7 @@ }, "filter_preprocessed_vcf": { "key": "filter_preprocessed_vcf", - "digest": "63mmofid6b46ugrq6hhmlpdc6htd767o", + "digest": "4jjtxpixe6gq6p3v7lnuyxhlzottg2ib", "tests": [ { "inputs": { From 8e62d96b4dbf408db2219902223fc110a501c479 Mon Sep 17 00:00:00 2001 From: William Rowell Date: Tue, 17 Dec 2024 17:12:00 -0800 Subject: [PATCH 16/22] Added test for exclusion of NO_READS. --- wdl-ci.config.json | 43 ++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 42 insertions(+), 1 deletion(-) diff --git a/wdl-ci.config.json b/wdl-ci.config.json index 134c417f..62f536cb 100644 --- a/wdl-ci.config.json +++ b/wdl-ci.config.json @@ -2415,7 +2415,7 @@ }, "run_pharmcat": { "key": "run_pharmcat", - "digest": "uknkltw6uwppbf5ttzrsifayz4pqplvi", + "digest": "", "tests": [ { "inputs": { @@ -2457,6 +2457,47 @@ ] } } + }, + { + "inputs": { + "preprocessed_filtered_vcf": "${resources_file_path}/run_pharmcat/input/HG002.GRCh38.subset.small_variants.preprocessed.filtered.vcf", + "input_tsvs": [ + "${resources_file_path}/run_pharmcat/input/HG002.NO_READS.pharmcat.tsv" + ], + "pharmcat_docker": "pgkb/pharmcat:2.15.4", + "out_prefix": "HG002.pharmcat", + "runtime_attributes": "${default_runtime_attributes}" + }, + "output_tests": { + "pharmcat_match_json": { + "value": "${resources_file_path}/run_pharmcat/output/NO_READS/HG002.pharmcat.match.json", + "test_tasks": [ + "compare_file_basename", + "check_json" + ] + }, + "pharmcat_phenotype_json": { + "value": "${resources_file_path}/run_pharmcat/output/NO_READS/HG002.pharmcat.phenotype.json", + "test_tasks": [ + "compare_file_basename", + "check_json" + ] + }, + "pharmcat_report_html": { + "value": "${resources_file_path}/run_pharmcat/output/NO_READS/HG002.pharmcat.report.html", + "test_tasks": [ + "compare_file_basename", + "check_html" + ] + }, + "pharmcat_report_json": { + "value": "${resources_file_path}/run_pharmcat/output/NO_READS/HG002.pharmcat.report.json", + "test_tasks": [ + "compare_file_basename", + "check_json" + ] + } + } } ] } From 1b76849536abffb2f8512ae47e1e09ee32ca4bb2 Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 18 Dec 2024 01:30:32 +0000 Subject: [PATCH 17/22] update wdl-ci config file after successful tests --- wdl-ci.config.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wdl-ci.config.json b/wdl-ci.config.json index 62f536cb..440db1ec 100644 --- a/wdl-ci.config.json +++ b/wdl-ci.config.json @@ -2415,7 +2415,7 @@ }, "run_pharmcat": { "key": "run_pharmcat", - "digest": "", + "digest": "uknkltw6uwppbf5ttzrsifayz4pqplvi", "tests": [ { "inputs": { From 34466b0edae6dcfc6bf1cd99f4a4dd6c64115255 Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 18 Dec 2024 20:34:18 +0000 Subject: [PATCH 18/22] update wdl-ci config file after successful tests --- wdl-ci.config.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wdl-ci.config.json b/wdl-ci.config.json index 440db1ec..6e82b2d2 100644 --- a/wdl-ci.config.json +++ b/wdl-ci.config.json @@ -2415,7 +2415,7 @@ }, "run_pharmcat": { "key": "run_pharmcat", - "digest": "uknkltw6uwppbf5ttzrsifayz4pqplvi", + "digest": "nsabvlc6qz2u6y7ikis4pa4oljfanewp", "tests": [ { "inputs": { From 91c07c769dce31a9d9100e73ad9327ffb27d7ad8 Mon Sep 17 00:00:00 2001 From: William Rowell Date: Fri, 10 Jan 2025 15:37:18 -0800 Subject: [PATCH 19/22] Update trgt coverage_dropouts task to use trgt v1.4.1 docker image. --- workflows/wdl-common | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/wdl-common b/workflows/wdl-common index 99b463b8..1c3c3384 160000 --- a/workflows/wdl-common +++ b/workflows/wdl-common @@ -1 +1 @@ -Subproject commit 99b463b8427f1158916705705fbdc998392c06be +Subproject commit 1c3c3384c106e6e60c035f281af773d59eae45ff From 945595675762fecf976abfeb73829efdcb04fd95 Mon Sep 17 00:00:00 2001 From: William Rowell Date: Fri, 10 Jan 2025 15:38:07 -0800 Subject: [PATCH 20/22] Update docs. --- README.md | 10 +++++----- docs/family.md | 8 ++++---- docs/pharmcat.md | 4 ++++ docs/singleton.md | 8 ++++---- docs/tools_containers.md | 30 +++++++++++++++--------------- image_manifest.txt | 4 ++-- 6 files changed, 34 insertions(+), 30 deletions(-) diff --git a/README.md b/README.md index 5de4588f..0b4029af 100644 --- a/README.md +++ b/README.md @@ -24,25 +24,25 @@ Both workflows are designed to analyze human PacBio whole genome sequencing (WGS This is an actively developed workflow with multiple versioned releases, and we make use of git submodules for common tasks that are shared by multiple workflows. There are two ways to ensure you are using a supported release of the workflow and ensure that the submodules are correctly initialized: -1) Download the release zips directly from a [supported release](https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/releases/tag/v2.0.7): +1) Download the release zips directly from a [supported release](https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/releases/tag/v2.1.0): ```bash - wget https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/releases/download/v2.0.7/hifi-human-wgs-singleton.zip - wget https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/releases/download/v2.0.7/hifi-human-wgs-family.zip + wget https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/releases/download/v2.1.0/hifi-human-wgs-singleton.zip + wget https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/releases/download/v2.1.0/hifi-human-wgs-family.zip ``` 2) Clone the repository and initialize the submodules: ```bash git clone \ - --depth 1 --branch v2.0.7 \ + --depth 1 --branch v2.1.0 \ --recursive \ https://github.com/PacificBiosciences/HiFi-human-WGS-WDL.git ``` ## Resource requirements -The most resource-heavy step in the workflow requires 64 cores and 256 GB of RAM. Ensure that the backend environment you're using has enough quota to run the workflow. +The most resource-heavy step in the workflow requires 64 cpu cores and 256 GB of RAM. Ensure that the backend environment you're using has enough quota to run the workflow. On some backends, you may be able to make use of a GPU to accelerate the DeepVariant step. The GPU is not required, but it can significantly speed up the workflow. If you have access to a GPU, you can set the `gpu` parameter to `true` in the inputs JSON file. diff --git a/docs/family.md b/docs/family.md index ed7fa7c2..4781c5b2 100644 --- a/docs/family.md +++ b/docs/family.md @@ -241,10 +241,10 @@ The `Sample` struct contains sample specific data and metadata. The struct has t | Type | Name | Description | Notes | | ---- | ---- | ----------- | ----- | | Array\[File\] | pbstarphase_json | PBstarPhase JSON | Haplotype calls for PGx loci | -| Array\[File\] | pharmcat_match_json | PharmCAT match JSON | | -| Array\[File\] | pharmcat_phenotype_json | PharmCAT phenotype JSON | | -| Array\[File\] | pharmcat_report_html | PharmCAT report HTML | | -| Array\[File\] | pharmcat_report_json | PharmCAT report JSON | | +| Array\[File?\] | pharmcat_match_json | PharmCAT match JSON | | +| Array\[File?\] | pharmcat_phenotype_json | PharmCAT phenotype JSON | | +| Array\[File?\] | pharmcat_report_html | PharmCAT report HTML | | +| Array\[File?\] | pharmcat_report_json | PharmCAT report JSON | | ### Tertiary Analysis diff --git a/docs/pharmcat.md b/docs/pharmcat.md index bcd11775..045da534 100644 --- a/docs/pharmcat.md +++ b/docs/pharmcat.md @@ -8,3 +8,7 @@ flowchart TD filter --> pharmcat["PharmCat"] pharmcat --> outputs[/"PharmCat outputs"/] ``` + +[PharmCat (Pharmacogenomics Clinical Annotation Tool)](https://pharmcat.org) analyzes genetic variants and predicts drug response. In this subworkflow implementation, PharmCat will use a combination of the small variant VCF and pbStarPhase outupts. PharmCat outputs will only be generated if the depth at the variant position is greater than `pharmcat_min_coverage` (default `10`). If no variants pass this filter, no outputs will be generated. + +Citation: K Sangkuhl & M Whirl-Carrillo, et al. Pharmacogenomics Clinical Annotation Tool (PharmCAT). Clinical Pharmacology & Therapeutics (2020) 107(1):203-210. [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6977333](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6977333). diff --git a/docs/singleton.md b/docs/singleton.md index 38c0bfe7..88fead95 100644 --- a/docs/singleton.md +++ b/docs/singleton.md @@ -200,10 +200,10 @@ flowchart TD | Type | Name | Description | Notes | | ---- | ---- | ----------- | ----- | | File | pbstarphase_json | PBstarPhase JSON | Haplotype calls for PGx loci | -| File | pharmcat_match_json | PharmCAT match JSON | | -| File | pharmcat_phenotype_json | PharmCAT phenotype JSON | | -| File | pharmcat_report_html | PharmCAT report HTML | | -| File | pharmcat_report_json | PharmCAT report JSON | | +| File? | pharmcat_match_json | PharmCAT match JSON | | +| File? | pharmcat_phenotype_json | PharmCAT phenotype JSON | | +| File? | pharmcat_report_html | PharmCAT report HTML | | +| File? | pharmcat_report_json | PharmCAT report JSON | | ### Tertiary Analysis diff --git a/docs/tools_containers.md b/docs/tools_containers.md index 2859cf05..adf0a895 100644 --- a/docs/tools_containers.md +++ b/docs/tools_containers.md @@ -4,26 +4,26 @@ Containers are used to package tools and their dependencies. This ensures that t Most of our containers are built on the `pb_wdl_base` container, which includes common bioinformatics tools and libraries. We tag our containers with a version number and build count, but the containers are referenced within the WDL files by the sha256 sum tags for reproducibility and better compatibility with Cromwell and miniwdl call caching. -Our Dockerfiles can be inspected on GitHub, and the containers can be pulled from our [Quay.io organization](https://quay.io/pacbio). +Our Dockerfiles can be inspected on GitHub, and the containers can be pulled from our [Quay.io organization](https://quay.io/repository/pacbio). We directly use `deepvariant`, `deepvariant-gpu`, `pharmcat`, and `glnexus` containers from their respective authors, although we have mirrored some for better compatibility with Cromwell call caching. | Container | Major tool versions | Dockerfile | Container | | --------: | ------------------- | :---: | :---: | -| pb_wdl_base |
  • htslib 1.20
  • bcftools 1.20
  • samtools 1.20
  • bedtools 2.31.0
  • python3.9
  • numpy 1.24.24
  • pandas 2.0.3
  • matplotlib 3.7.5
  • seaborn 0.13.2
  • pysam 0.22.1
  • vcfpy 0.13.8
  • biopython 1.83
| [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/6b13cc246dd44e41903d17a660bb5432cdd18dbe/docker/pb_wdl_base) | [sha256:4b889a1f21a6a7fecf18820613cf610103966a93218de772caba126ab70a8e87](https://quay.io/pacbio/pb_wdl_base/manifest/pb_wdl_base@sha256:4b889a1f21a6a7fecf18820613cf610103966a93218de772caba126ab70a8e87) | -| pbmm2 |
  • pbmm2 1.16.0
| [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/44df87558e18ce9d3b65f3ede9c7ba1513669ccb/docker/pbmm2) | [pbmm2@sha256:24218cb5cbc68d1fd64db14a9dc38263d3d931c74aca872c998d12ef43020ef0](https://quay.io/pacbio/pbmm2/manifest/sha256:24218cb5cbc68d1fd64db14a9dc38263d3d931c74aca872c998d12ef43020ef0) | -| mosdepth |
  • mosdepth 0.3.9
| [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/fa84fbf582738c05c750e667ff43d11552ad4183/docker/mosdepth) | [mosdepth@sha256:63f7a5d1a4a17b71e66d755d3301a951e50f6b63777d34dab3ee9e182fd7acb1](https://quay.io/pacbio/mosdepth/manifest/sha256:63f7a5d1a4a17b71e66d755d3301a951e50f6b63777d34dab3ee9e182fd7acb1) | -| pbsv |
  • pbsv 2.10.0
| [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/e82dddf32b042e985a5d66d0ebe25ca57058e61c/docker/pbsv) | [pbsv@sha256:3a8529853c1e214809dcdaacac0079de70d0c037b41b43bb8ba7c3fc5f783e26](https://quay.io/pacbio/pbsv/manifest/sha256:3a8529853c1e214809dcdaacac0079de70d0c037b41b43bb8ba7c3fc5f783e26) | -| trgt |
  • trgt 1.2.0
  • `/opt/scripts/check_trgt_coverage.py` 0.1.0
| [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/ed658e93fc51229f20415e0784dc242a8e4ef66a/docker/trgt) | [trgt@sha256:0284ff5756f8d47d9d81b515b8b1a6c81fac862ae5a7b4fe89f65235c3e5e0c9](https://quay.io/pacbio/trgt/manifest/sha256:0284ff5756f8d47d9d81b515b8b1a6c81fac862ae5a7b4fe89f65235c3e5e0c9) | -| hiphase |
  • hiphase 1.4.5
| [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/1051d12818e165a2145526e0b58f0ed0d0dc023a/docker/hiphase) | [hiphase@sha256:47fe7d42aea6b1b2e6d3c7401bc35a184464c3f647473d0525c00f3c968b40ad](https://quay.io/pacbio/hiphase/manifest/sha256:47fe7d42aea6b1b2e6d3c7401bc35a184464c3f647473d0525c00f3c968b40ad) | -| hificnv |
  • hificnv 1.0.1
| [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/a58f8b44cf8fd09c39c90e07076dbb418188084d/docker/hificnv) | [hificnv@sha256:c4764a70c8c2028edb1cdb4352997269947c5076ddd1aeaeef6c5076c630304d](https://quay.io/pacbio/hificnv/manifest/sha256:c4764a70c8c2028edb1cdb4352997269947c5076ddd1aeaeef6c5076c630304d) | -| paraphase |
  • paraphase 3.1.1
  • minimap 2.28
| [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/6b13cc246dd44e41903d17a660bb5432cdd18dbe/docker/paraphase) | [paraphase@sha256:a114ac5b9a682d7dc0fdf25c92cfb36f80c07ab4f1fb76b2e58092521b123a4d](https://quay.io/pacbio/paraphase/manifest/sha256:a114ac5b9a682d7dc0fdf25c92cfb36f80c07ab4f1fb76b2e58092521b123a4d) | -| pbstarphase |
  • pbstarphase 1.0.0
  • Database 20240826
| [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/813c7dc3143b91c34754d768c3e27a46355bb3e5/docker/pbstarphase) | [pbstarphase@sha256:6954d6f7e462c9cec7aaf7ebb66efaf13d448239aab76a3c947c1dfe24859686](https://quay.io/pacbio/pbstarphase/manifest/sha256:6954d6f7e462c9cec7aaf7ebb66efaf13d448239aab76a3c947c1dfe24859686) | -| pb-cpg-tools |
  • pb-cpg-tools 2.3.2
| [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/6b13cc246dd44e41903d17a660bb5432cdd18dbe/docker/pb-cpg-tools) | [pb-cpg-tools@sha256:d6e63fe3f6855cfe60f573de1ca85fab27f4a68e24a7f5691a7a805a22af292d](https://quay.io/pacbio/pb-cpg-tools/manifest/sha256:d6e63fe3f6855cfe60f573de1ca85fab27f4a68e24a7f5691a7a805a22af292d) | -| wgs_tertiary |
  • `/opt/scripts/calculate_phrank.py` 2.0.0
  • `/opt/scripts/json2ped.py` 0.5.0
Last built 2021-09-17:
  • ensembl -> HGNC
  • ensembl -> HPO
  • HGNC -> inheritance
  • HPO DAG
| [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/fd70e2872bd3c6bb705faff5bc68374116d7d62f/docker/wgs_tertiary) | [wgs_tertiary@sha256:410597030e0c85cf16eb27a877d260e7e2824747f5e8b05566a1aaa729d71136](https://quay.io/pacbio/wgs_tertiary/manifest/sha256:410597030e0c85cf16eb27a877d260e7e2824747f5e8b05566a1aaa729d71136) | -| slivar |
  • slivar 0.3.1
  • `/opt/scripts/add_comphet_phase.py` 0.1.0
| [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/5e1094fd6755203b4971fdac6dcb951bbc098bed/docker/slivar) | [slivar@sha256:35be557730d3ac9e883f1c2010fb24ac02631922f9b4948b0608d3e643a46e8b](https://quay.io/pacbio/slivar/manifest/sha256:35be557730d3ac9e883f1c2010fb24ac02631922f9b4948b0608d3e643a46e8b) | -| svpack |
  • svpack 54b54db
| [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/6fc750b0c65b4a5c1eb65791eab9eed89864d858/docker/svpack) | [svpack@sha256:628e9851e425ed8044a907d33de04043d1ef02d4d2b2667cf2e9a389bb011eba](https://quay.io/pacbio/svpack/manifest/sha256:628e9851e425ed8044a907d33de04043d1ef02d4d2b2667cf2e9a389bb011eba) | +| pb_wdl_base |
  • htslib 1.20
  • bcftools 1.20
  • samtools 1.20
  • bedtools 2.31.0
  • python3.9
  • numpy 1.24.24
  • pandas 2.0.3
  • matplotlib 3.7.5
  • seaborn 0.13.2
  • pysam 0.22.1
  • vcfpy 0.13.8
  • biopython 1.83
| [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/6b13cc246dd44e41903d17a660bb5432cdd18dbe/docker/pb_wdl_base) | [sha256:4b889a1f21a6a7fecf18820613cf610103966a93218de772caba126ab70a8e87](https://quay.io/repository/pacbio/pb_wdl_base/manifest/pb_wdl_base@sha256:4b889a1f21a6a7fecf18820613cf610103966a93218de772caba126ab70a8e87) | +| pbmm2 |
  • pbmm2 1.16.99
| [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/613e2f8bce34a15ccdfc52572fe1a6c3458be397/docker/pbmm2) | [pbmm2@sha256:b58eef0645dd9adca850c9b4811f289ddcd57f630596d9f524701bc787467f30](https://quay.io/repository/pacbio/pbmm2/manifest/sha256:b58eef0645dd9adca850c9b4811f289ddcd57f630596d9f524701bc787467f30) | +| mosdepth |
  • mosdepth 0.3.9
| [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/fa84fbf582738c05c750e667ff43d11552ad4183/docker/mosdepth) | [mosdepth@sha256:63f7a5d1a4a17b71e66d755d3301a951e50f6b63777d34dab3ee9e182fd7acb1](https://quay.io/repository/pacbio/mosdepth/manifest/sha256:63f7a5d1a4a17b71e66d755d3301a951e50f6b63777d34dab3ee9e182fd7acb1) | +| pbsv |
  • pbsv 2.10.0
| [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/e82dddf32b042e985a5d66d0ebe25ca57058e61c/docker/pbsv) | [pbsv@sha256:3a8529853c1e214809dcdaacac0079de70d0c037b41b43bb8ba7c3fc5f783e26](https://quay.io/repository/pacbio/pbsv/manifest/sha256:3a8529853c1e214809dcdaacac0079de70d0c037b41b43bb8ba7c3fc5f783e26) | +| trgt |
  • trgt 1.4.1
  • `/opt/scripts/check_trgt_coverage.py` 0.1.0
| [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/d7fe03e8ab11d58febe7ad29bfafc5ade8cc868c/docker/trgt) | [trgt@sha256:109134f94756b190f2ba8dad3ed9f1ce4b9048247f6fafc7a7c35daab07a91be](https://quay.io/repository/pacbio/trgt/manifest/sha256:109134f94756b190f2ba8dad3ed9f1ce4b9048247f6fafc7a7c35daab07a91be) | +| hiphase |
  • hiphase 1.4.5
| [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/1051d12818e165a2145526e0b58f0ed0d0dc023a/docker/hiphase) | [hiphase@sha256:47fe7d42aea6b1b2e6d3c7401bc35a184464c3f647473d0525c00f3c968b40ad](https://quay.io/repository/pacbio/hiphase/manifest/sha256:47fe7d42aea6b1b2e6d3c7401bc35a184464c3f647473d0525c00f3c968b40ad) | +| hificnv |
  • hificnv 1.0.1
| [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/a58f8b44cf8fd09c39c90e07076dbb418188084d/docker/hificnv) | [hificnv@sha256:c4764a70c8c2028edb1cdb4352997269947c5076ddd1aeaeef6c5076c630304d](https://quay.io/repository/pacbio/hificnv/manifest/sha256:c4764a70c8c2028edb1cdb4352997269947c5076ddd1aeaeef6c5076c630304d) | +| paraphase |
  • paraphase 3.1.1
  • minimap 2.28
| [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/6b13cc246dd44e41903d17a660bb5432cdd18dbe/docker/paraphase) | [paraphase@sha256:a114ac5b9a682d7dc0fdf25c92cfb36f80c07ab4f1fb76b2e58092521b123a4d](https://quay.io/repository/pacbio/paraphase/manifest/sha256:a114ac5b9a682d7dc0fdf25c92cfb36f80c07ab4f1fb76b2e58092521b123a4d) | +| pbstarphase |
  • pbstarphase 1.0.0
  • Database 20240826
| [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/813c7dc3143b91c34754d768c3e27a46355bb3e5/docker/pbstarphase) | [pbstarphase@sha256:6954d6f7e462c9cec7aaf7ebb66efaf13d448239aab76a3c947c1dfe24859686](https://quay.io/repository/pacbio/pbstarphase/manifest/sha256:6954d6f7e462c9cec7aaf7ebb66efaf13d448239aab76a3c947c1dfe24859686) | +| pb-cpg-tools |
  • pb-cpg-tools 2.3.2
| [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/6b13cc246dd44e41903d17a660bb5432cdd18dbe/docker/pb-cpg-tools) | [pb-cpg-tools@sha256:d6e63fe3f6855cfe60f573de1ca85fab27f4a68e24a7f5691a7a805a22af292d](https://quay.io/repository/pacbio/pb-cpg-tools/manifest/sha256:d6e63fe3f6855cfe60f573de1ca85fab27f4a68e24a7f5691a7a805a22af292d) | +| wgs_tertiary |
  • `/opt/scripts/calculate_phrank.py` 2.0.0
  • `/opt/scripts/json2ped.py` 0.5.0
Last built 2021-09-17:
  • ensembl -> HGNC
  • ensembl -> HPO
  • HGNC -> inheritance
  • HPO DAG
| [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/fd70e2872bd3c6bb705faff5bc68374116d7d62f/docker/wgs_tertiary) | [wgs_tertiary@sha256:410597030e0c85cf16eb27a877d260e7e2824747f5e8b05566a1aaa729d71136](https://quay.io/repository/pacbio/wgs_tertiary/manifest/sha256:410597030e0c85cf16eb27a877d260e7e2824747f5e8b05566a1aaa729d71136) | +| slivar |
  • slivar 0.3.1
  • `/opt/scripts/add_comphet_phase.py` 0.1.0
| [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/5e1094fd6755203b4971fdac6dcb951bbc098bed/docker/slivar) | [slivar@sha256:35be557730d3ac9e883f1c2010fb24ac02631922f9b4948b0608d3e643a46e8b](https://quay.io/repository/pacbio/slivar/manifest/sha256:35be557730d3ac9e883f1c2010fb24ac02631922f9b4948b0608d3e643a46e8b) | +| svpack |
  • svpack 54b54db
| [Dockerfile](https://github.com/PacificBiosciences/wdl-dockerfiles/tree/6fc750b0c65b4a5c1eb65791eab9eed89864d858/docker/svpack) | [svpack@sha256:628e9851e425ed8044a907d33de04043d1ef02d4d2b2667cf2e9a389bb011eba](https://quay.io/repository/pacbio/svpack/manifest/sha256:628e9851e425ed8044a907d33de04043d1ef02d4d2b2667cf2e9a389bb011eba) | | deepvariant |
  • DeepVariant 1.6.1
| | [deepvariant:1.6.1](https://hub.docker.com/layers/google/deepvariant/1.6.1/images/sha256-ccab95548e6c3ec28c75232987f31209ff1392027d67732435ce1ba3d0b55c68) | | deepvariant-gpu |
  • DeepVariant 1.6.1
| | [deepvariant:1.6.1-gpu](https://hub.docker.com/layers/google/deepvariant/1.6.1-gpu/images/sha256-7929c55106d3739daa18d52802913c43af4ca2879db29656056f59005d1d46cb) | | pharmcat |
  • PharmCat 2.15.4
| | [pharmcat:2.15.4](https://hub.docker.com/layers/pgkb/pharmcat/2.15.4/images/sha256-5b58ae959b4cd85986546c2d67e3596f33097dedc40dfe57dd845b6e78781eb6) | -| glnexus |
  • GLnexus 1.4.3
| | [glnexus:1.4.3](https://quay.io/pacbio/glnexus/manifest/sha256:ce6fecf59dddc6089a8100b31c29c1e6ed50a0cf123da9f2bc589ee4b0c69c8e) | +| glnexus |
  • GLnexus 1.4.3
| | [glnexus:1.4.3](https://quay.io/repository/pacbio/glnexus/manifest/sha256:ce6fecf59dddc6089a8100b31c29c1e6ed50a0cf123da9f2bc589ee4b0c69c8e) | diff --git a/image_manifest.txt b/image_manifest.txt index 4ac72408..05af65dd 100644 --- a/image_manifest.txt +++ b/image_manifest.txt @@ -4,13 +4,13 @@ quay.io/pacbio/hiphase@sha256:47fe7d42aea6b1b2e6d3c7401bc35a184464c3f647473d0525 quay.io/pacbio/mosdepth@sha256:63f7a5d1a4a17b71e66d755d3301a951e50f6b63777d34dab3ee9e182fd7acb1 quay.io/pacbio/paraphase@sha256:a114ac5b9a682d7dc0fdf25c92cfb36f80c07ab4f1fb76b2e58092521b123a4d quay.io/pacbio/pb-cpg-tools@sha256:d6e63fe3f6855cfe60f573de1ca85fab27f4a68e24a7f5691a7a805a22af292d -quay.io/pacbio/pbmm2@sha256:24218cb5cbc68d1fd64db14a9dc38263d3d931c74aca872c998d12ef43020ef0 +quay.io/pacbio/pbmm2@sha256:b58eef0645dd9adca850c9b4811f289ddcd57f630596d9f524701bc787467f30 quay.io/pacbio/pbstarphase@sha256:6954d6f7e462c9cec7aaf7ebb66efaf13d448239aab76a3c947c1dfe24859686 quay.io/pacbio/pbsv@sha256:3a8529853c1e214809dcdaacac0079de70d0c037b41b43bb8ba7c3fc5f783e26 quay.io/pacbio/pb_wdl_base@sha256:4b889a1f21a6a7fecf18820613cf610103966a93218de772caba126ab70a8e87 quay.io/pacbio/slivar@sha256:f71a27f756e2d69ec30949cbea97c54abbafde757562a98ef965f21a28aa8eaa quay.io/pacbio/svpack@sha256:628e9851e425ed8044a907d33de04043d1ef02d4d2b2667cf2e9a389bb011eba -quay.io/pacbio/trgt@sha256:0284ff5756f8d47d9d81b515b8b1a6c81fac862ae5a7b4fe89f65235c3e5e0c9 +quay.io/pacbio/trgt@sha256:109134f94756b190f2ba8dad3ed9f1ce4b9048247f6fafc7a7c35daab07a91be quay.io/pacbio/wgs_tertiary@sha256:410597030e0c85cf16eb27a877d260e7e2824747f5e8b05566a1aaa729d71136 google/deepvariant:1.6.1 google/deepvariant:1.6.1-gpu From 507d6bfeda85a1394edb4ca16e7f0f1bf28a7286 Mon Sep 17 00:00:00 2001 From: William Rowell Date: Fri, 10 Jan 2025 15:38:31 -0800 Subject: [PATCH 21/22] Update documentation for #178 --- docs/backend-hpc.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/docs/backend-hpc.md b/docs/backend-hpc.md index acd5bb71..c2033910 100644 --- a/docs/backend-hpc.md +++ b/docs/backend-hpc.md @@ -13,6 +13,14 @@ Either `miniwdl` or `Cromwell` can be used to run workflows on the HPC. An [example miniwdl.cfg file](https://github.com/PacificBiosciences/HiFi-human-WGS-WDL/blob/main/backends/hpc/miniwdl.cfg) is provided here. This should be placed at `~/.config/miniwdl.cfg` and edited to match your slurm configuration. This allows running workflows using a basic SLURM setup. +> [!IMPORTANT] +> In order to simplify workflow inputs, we make use of `map` files to specify the input data. This allows for a more concise input file, but requires changing a miniwdl configuration option to allow workflows to access files that are not expressly supplied with workflow inputs. To enable this, add the following line to your `miniwdl.cfg` file: +> ```ini +> [file_io] +> allow_any_input = true +> ``` +> This option is already included in the example miniwdl.cfg file described in this section. + ## Installing and configuring `Cromwell` Cromwell supports a number of different HPC backends; see [Cromwell's documentation](https://cromwell.readthedocs.io/en/stable/backends/HPC/) for more information on configuring each of the backends. Cromwell can be used in a standalone "run" mode, or in "server" mode to allow for multiple users to submit workflows. In the example below, we provide example commands for running Cromwell in "run" mode. From 24ce2280c57d3b0b62571cc16ca30c04a21e93c7 Mon Sep 17 00:00:00 2001 From: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Date: Fri, 10 Jan 2025 23:46:27 +0000 Subject: [PATCH 22/22] update wdl-ci config file after successful tests --- wdl-ci.config.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wdl-ci.config.json b/wdl-ci.config.json index 6e82b2d2..f2c69d9f 100644 --- a/wdl-ci.config.json +++ b/wdl-ci.config.json @@ -1801,7 +1801,7 @@ }, "coverage_dropouts": { "key": "coverage_dropouts", - "digest": "k6fkzuz3gk4yqc555nov2io3qbeqe25h", + "digest": "766oizl5v2zadfp5bhmkds52ww6z75ov", "tests": [ { "inputs": {