From 715123f816e7edffb88ee7f86903a7c52e94e0fe Mon Sep 17 00:00:00 2001 From: Curtis Kapsak Date: Thu, 9 Mar 2023 10:39:23 -0500 Subject: [PATCH] update default pangolin docker to staphb/pangolin:4.2-pdata-1.18.1.1 and nextclade_dataset_tag for SC2 (#217) * update default pangolin docker to staphb/pangolin:4.2-pdata-1.18.1.1; also updated phvg to v2.3.1 * update default nextclade_dataset_tag to 2023-02-25T12:00:00Z for theiacov CL, ILMN PE, ILMN SE, ONT, and FASTA workflow. Tag is only compatible with SC2, NOT the other organisms * update CI for theiacov_illumina_pe and se * update hash for call-nextclade_one_sample * update has for call-nextclade_one_sample * update has for call-pangolin4 * update has for pangolin4 * update has for call-pangolin4 * update has for task_taxonID * update has for task_versioning * update has for theiacov_ont * CI changes for theiacov clearlabs --------- Co-authored-by: frankambrosio3 --- tasks/task_taxonID.wdl | 2 +- tasks/task_versioning.wdl | 2 +- tests/workflows/test_clearlabs.yml | 16 ++++++++-------- tests/workflows/test_illumina_pe.yml | 16 ++++++++-------- tests/workflows/test_illumina_se.yml | 16 ++++++++-------- tests/workflows/test_ont.yml | 16 ++++++++-------- workflows/wf_theiacov_clearlabs.wdl | 2 +- workflows/wf_theiacov_fasta.wdl | 2 +- workflows/wf_theiacov_illumina_pe.wdl | 2 +- workflows/wf_theiacov_illumina_se.wdl | 2 +- workflows/wf_theiacov_ont.wdl | 2 +- 11 files changed, 39 insertions(+), 39 deletions(-) diff --git a/tasks/task_taxonID.wdl b/tasks/task_taxonID.wdl index ea8a690f..a39c8f0c 100644 --- a/tasks/task_taxonID.wdl +++ b/tasks/task_taxonID.wdl @@ -144,7 +144,7 @@ task pangolin4 { String samplename Int min_length = 10000 Float max_ambig = 0.5 - String docker = "staphb/pangolin:4.1.3-pdata-1.17" + String docker = "staphb/pangolin:4.2-pdata-1.18.1.1" String? analysis_mode Boolean expanded_lineage=true Boolean skip_scorpio=false diff --git a/tasks/task_versioning.wdl b/tasks/task_versioning.wdl index 530c9523..22606fa5 100644 --- a/tasks/task_versioning.wdl +++ b/tasks/task_versioning.wdl @@ -9,7 +9,7 @@ task version_capture { volatile: true } command <<< - PHVG_Version="PHVG 2.3.0" + PHVG_Version="PHVG 2.3.1" ~{default='' 'export TZ=' + timezone} date +"%Y-%m-%d" > TODAY echo $PHVG_Version > PHVG_VERSION diff --git a/tests/workflows/test_clearlabs.yml b/tests/workflows/test_clearlabs.yml index c24632c7..f436f93b 100644 --- a/tests/workflows/test_clearlabs.yml +++ b/tests/workflows/test_clearlabs.yml @@ -212,7 +212,7 @@ - path: miniwdl_run/call-ncbi_scrub_se/work/r1.fastq.clean md5sum: 033e7bdb8c34ed0df11bf9f604addb54 - path: miniwdl_run/call-nextclade_one_sample/command - md5sum: cbbe0dff285557074640df4d18205e1d + md5sum: 2705013ff67c2e6ecf7a9358ee52d3b7 - path: miniwdl_run/call-nextclade_one_sample/inputs.json contains: ["dataset_name", "dataset_tag", "genome_fasta"] - path: miniwdl_run/call-nextclade_one_sample/outputs.json @@ -314,15 +314,15 @@ - path: miniwdl_run/call-pangolin4/work/PANGOLIN_LINEAGE md5sum: 717da6cd0df2d2f1d00461f3498aaca9 - path: miniwdl_run/call-pangolin4/work/PANGOLIN_NOTES - md5sum: 0d654329677a43e9626ea3921b924662 + md5sum: 3cf7fd185fe58af5952d52e91d4805c0 - path: miniwdl_run/call-pangolin4/work/PANGO_ASSIGNMENT_VERSION - md5sum: 4e434d75ffecbd1669b89698d0f74d9e + md5sum: 983fed7641ec9e1b2d258ee1184dd75c - path: miniwdl_run/call-pangolin4/work/VERSION_PANGOLIN_ALL - md5sum: 610311d600672ebc0fb9c138cab9945a + md5sum: 73197f226b6f9ce6f0090d3eb41a9861 - path: miniwdl_run/call-pangolin4/work/_miniwdl_inputs/0/clearlabs.medaka.consensus.fasta md5sum: d41d8cd98f00b204e9800998ecf8427e - path: miniwdl_run/call-pangolin4/work/clearlabs.pangolin_report.csv - md5sum: 8f98ee098c10003b1a04cb13493aec78 + md5sum: 45841b0ac927345415c485d363bb5f45 - path: miniwdl_run/call-sc2_gene_coverage/command md5sum: 7090d929e3e59de1b4799d44824bf1d3 - path: miniwdl_run/call-sc2_gene_coverage/inputs.json @@ -486,11 +486,11 @@ - path: miniwdl_run//wdl/tasks/task_sc2_gene_coverage.wdl md5sum: e8310700d96d98cd16f4859f61dd179f - path: miniwdl_run/wdl/tasks/task_taxonID.wdl - md5sum: 6754daa67e78f8d2497610b9f6005ad5 + md5sum: d7db51677d9904efb480993f64dc4410 - path: miniwdl_run/wdl/tasks/task_versioning.wdl - md5sum: 27d436979d253be67940a84696c5b77b + md5sum: ad14ec780a96c09a1f865773395da0f7 - path: miniwdl_run/wdl/workflows/wf_theiacov_clearlabs.wdl - md5sum: 07a499e0e363f2cc339618002b98c38a + md5sum: aa6d9846fba576a77d270d4d536c4984 - path: miniwdl_run/inputs.json contains: ["theiacov_clearlabs", "samplename", "primer_bed"] - path: miniwdl_run/outputs.json diff --git a/tests/workflows/test_illumina_pe.yml b/tests/workflows/test_illumina_pe.yml index 767f43f8..2f7b9610 100644 --- a/tests/workflows/test_illumina_pe.yml +++ b/tests/workflows/test_illumina_pe.yml @@ -84,7 +84,7 @@ - path: miniwdl_run/call-consensus_qc/work/_miniwdl_inputs/0/SRR13687078.ivar.consensus.fasta md5sum: d41d8cd98f00b204e9800998ecf8427e - path: miniwdl_run/call-nextclade_one_sample_run1/command - md5sum: 539873fddb3b5b73b99f08d0c7959943 + md5sum: 68ed04af15a6717e9931950dab49a05d - path: miniwdl_run/call-nextclade_one_sample_run1/inputs.json contains: ["dataset_name", "genome_fasta", "SRR13687078"] - path: miniwdl_run/call-nextclade_one_sample_run1/outputs.json @@ -186,13 +186,13 @@ - path: miniwdl_run/call-pangolin4/work/PANGOLIN_LINEAGE md5sum: 655588ced8f4fc5d312ed152492d6bb0 - path: miniwdl_run/call-pangolin4/work/PANGOLIN_NOTES - md5sum: c72695b331cf7d87edfebc08f903b081 + md5sum: e98d2fc28664c0622f6b490433286e32 - path: miniwdl_run/call-pangolin4/work/PANGO_ASSIGNMENT_VERSION - md5sum: 4e434d75ffecbd1669b89698d0f74d9e + md5sum: 983fed7641ec9e1b2d258ee1184dd75c - path: miniwdl_run/call-pangolin4/work/SRR13687078.pangolin_report.csv - md5sum: 47c00bf9759206ee2867357501bed615 + md5sum: fe6a37d2d5b9c492e2a0da1a2c90231c - path: miniwdl_run/call-pangolin4/work/VERSION_PANGOLIN_ALL - md5sum: 610311d600672ebc0fb9c138cab9945a + md5sum: 73197f226b6f9ce6f0090d3eb41a9861 - path: miniwdl_run/call-pangolin4/work/_miniwdl_inputs/0/SRR13687078.ivar.consensus.fasta md5sum: d41d8cd98f00b204e9800998ecf8427e - path: miniwdl_run/call-primer_trim/command @@ -602,13 +602,13 @@ - path: miniwdl_run/wdl/tasks/task_sc2_gene_coverage.wdl md5sum: e8310700d96d98cd16f4859f61dd179f - path: miniwdl_run/wdl/tasks/task_taxonID.wdl - md5sum: 6754daa67e78f8d2497610b9f6005ad5 + md5sum: d7db51677d9904efb480993f64dc4410 - path: miniwdl_run/wdl/tasks/task_versioning.wdl - md5sum: 27d436979d253be67940a84696c5b77b + md5sum: ad14ec780a96c09a1f865773395da0f7 - path: miniwdl_run/wdl/workflows/wf_read_QC_trim.wdl md5sum: 9769f7ff548537ed7d36c5d0df445416 - path: miniwdl_run/wdl/workflows/wf_theiacov_illumina_pe.wdl - md5sum: 3bdb5271010f30059416aee2ee44dbd5 + md5sum: e12e61c3c5a9add46a04d0a0c11961e7 - path: miniwdl_run/inputs.json contains: ["theiacov_illumina_pe", "samplename", "primer_bed"] - path: miniwdl_run/outputs.json diff --git a/tests/workflows/test_illumina_se.yml b/tests/workflows/test_illumina_se.yml index 1583ea0e..00f98944 100644 --- a/tests/workflows/test_illumina_se.yml +++ b/tests/workflows/test_illumina_se.yml @@ -83,7 +83,7 @@ - path: miniwdl_run/call-consensus_qc/work/_miniwdl_inputs/0/ERR6319327.ivar.consensus.fasta md5sum: d41d8cd98f00b204e9800998ecf8427e - path: miniwdl_run/call-nextclade_one_sample/command - md5sum: 00d8320c74e760d6281acf5d4764c504 + md5sum: fd161e7657dabd1b488f1871a4b15b91 - path: miniwdl_run/call-nextclade_one_sample/inputs.json contains: ["dataset_name", "genome_fasta", "ERR6319327"] - path: miniwdl_run/call-nextclade_one_sample/outputs.json @@ -180,7 +180,7 @@ contains: ["wdl", "theiacov_illumina_se", "pangolin", "done"] - path: miniwdl_run/call-pangolin4/work/DATE - path: miniwdl_run/call-pangolin4/work/ERR6319327.pangolin_report.csv - md5sum: 29a1f778b2387ddb31aedf2627e2c895 + md5sum: 20ecd592059c5c10695d7c039ace61c9 - path: miniwdl_run/call-pangolin4/work/EXPANDED_LINEAGE md5sum: 2430b919e9b5f418c6a13add9d3c1db8 - path: miniwdl_run/call-pangolin4/work/PANGOLIN_CONFLICTS @@ -188,11 +188,11 @@ - path: miniwdl_run/call-pangolin4/work/PANGOLIN_LINEAGE md5sum: 2430b919e9b5f418c6a13add9d3c1db8 - path: miniwdl_run/call-pangolin4/work/PANGOLIN_NOTES - md5sum: 26668c8b0624d99676391b00c9775d2a + md5sum: 0b1f8fb5b938fe71631f61234cbf7ab3 - path: miniwdl_run/call-pangolin4/work/PANGO_ASSIGNMENT_VERSION - md5sum: 4e434d75ffecbd1669b89698d0f74d9e + md5sum: 983fed7641ec9e1b2d258ee1184dd75c - path: miniwdl_run/call-pangolin4/work/VERSION_PANGOLIN_ALL - md5sum: 610311d600672ebc0fb9c138cab9945a + md5sum: 73197f226b6f9ce6f0090d3eb41a9861 - path: miniwdl_run/call-pangolin4/work/_miniwdl_inputs/0/ERR6319327.ivar.consensus.fasta md5sum: d41d8cd98f00b204e9800998ecf8427e - path: miniwdl_run/call-primer_trim/command @@ -512,13 +512,13 @@ - path: miniwdl_run/wdl/tasks/task_sc2_gene_coverage.wdl md5sum: e8310700d96d98cd16f4859f61dd179f - path: miniwdl_run/wdl/tasks/task_taxonID.wdl - md5sum: 6754daa67e78f8d2497610b9f6005ad5 + md5sum: d7db51677d9904efb480993f64dc4410 - path: miniwdl_run/wdl/tasks/task_versioning.wdl - md5sum: 27d436979d253be67940a84696c5b77b + md5sum: ad14ec780a96c09a1f865773395da0f7 - path: miniwdl_run/wdl/workflows/wf_read_QC_trim_se.wdl md5sum: eb4170a3da9d95720b5403dd3d5e5d87 - path: miniwdl_run/wdl/workflows/wf_theiacov_illumina_se.wdl - md5sum: 2ae893ceba2cfa4f579bb086c9ffddd9 + md5sum: 9a21fa9bcb0c58692e4a5a5b03a0b56c - path: miniwdl_run/inputs.json contains: ["theiacov_illumina_se", "samplename", "primer_bed"] - path: miniwdl_run/outputs.json diff --git a/tests/workflows/test_ont.yml b/tests/workflows/test_ont.yml index 1ac2114b..8c2905a1 100644 --- a/tests/workflows/test_ont.yml +++ b/tests/workflows/test_ont.yml @@ -208,7 +208,7 @@ - path: miniwdl_run/call-ncbi_scrub_se/work/r1.fastq.clean md5sum: 2cf5f8defc05395fecd10c68865f9ae3 - path: miniwdl_run/call-nextclade_one_sample/command - md5sum: 31d0fad6de95d8c19c087552113fe3fa + md5sum: 60ba5d41705947d7ada8df00dd53d0b9 - path: miniwdl_run/call-nextclade_one_sample/inputs.json contains: ["dataset_name", "dataset_tag", "genome_fasta"] - path: miniwdl_run/call-nextclade_one_sample/outputs.json @@ -235,7 +235,7 @@ - path: miniwdl_run/call-nextclade_one_sample/work/nextclade_dataset_dir/primers.csv md5sum: 5990c3483bf66ce607aeb90a44e7ef2e - path: miniwdl_run/call-nextclade_one_sample/work/nextclade_dataset_dir/qc.json - md5sum: 518c01e982a20712d67fafb5c5fc953c + md5sum: 6587a54553ad565d5f8ea7d214a797d4 - path: miniwdl_run/call-nextclade_one_sample/work/nextclade_dataset_dir/reference.fasta md5sum: c7ce05f28e4ec0322c96f24e064ef55c - path: miniwdl_run/call-nextclade_one_sample/work/nextclade_dataset_dir/sequences.fasta @@ -313,13 +313,13 @@ - path: miniwdl_run/call-pangolin4/work/PANGOLIN_NOTES md5sum: 35aa27af5fb90d54561ee9d45a3163d5 - path: miniwdl_run/call-pangolin4/work/PANGO_ASSIGNMENT_VERSION - md5sum: 4e434d75ffecbd1669b89698d0f74d9e + md5sum: 983fed7641ec9e1b2d258ee1184dd75c - path: miniwdl_run/call-pangolin4/work/VERSION_PANGOLIN_ALL - md5sum: 610311d600672ebc0fb9c138cab9945a + md5sum: 73197f226b6f9ce6f0090d3eb41a9861 - path: miniwdl_run/call-pangolin4/work/_miniwdl_inputs/0/ont.medaka.consensus.fasta md5sum: d41d8cd98f00b204e9800998ecf8427e - path: miniwdl_run/call-pangolin4/work/ont.pangolin_report.csv - md5sum: b7b9dcced52783d5153dc469971be4fe + md5sum: 65a9cb959d8749684c00bdc65626f4d8 - path: miniwdl_run/call-read_filtering/command md5sum: 5a9e0fdba76808aef9f652244d355675 - path: miniwdl_run/call-read_filtering/inputs.json @@ -494,11 +494,11 @@ - path: miniwdl_run/wdl/tasks/task_sc2_gene_coverage.wdl md5sum: e8310700d96d98cd16f4859f61dd179f - path: miniwdl_run/wdl/tasks/task_taxonID.wdl - md5sum: 6754daa67e78f8d2497610b9f6005ad5 + md5sum: d7db51677d9904efb480993f64dc4410 - path: miniwdl_run/wdl/tasks/task_versioning.wdl - md5sum: 27d436979d253be67940a84696c5b77b + md5sum: ad14ec780a96c09a1f865773395da0f7 - path: miniwdl_run/wdl/workflows/wf_theiacov_ont.wdl - md5sum: ebee7984a3c2326d0dff24af80f57665 + md5sum: 6a0d307ba69dd3793a1be8d512e99b54 - path: miniwdl_run/inputs.json contains: ["theiacov_ont", "samplename", "primer_bed"] - path: miniwdl_run/outputs.json diff --git a/workflows/wf_theiacov_clearlabs.wdl b/workflows/wf_theiacov_clearlabs.wdl index 3f594fa1..c02e2d3d 100644 --- a/workflows/wf_theiacov_clearlabs.wdl +++ b/workflows/wf_theiacov_clearlabs.wdl @@ -21,7 +21,7 @@ workflow theiacov_clearlabs { File primer_bed Int normalise = 20000 String nextclade_dataset_reference = "MN908947" - String nextclade_dataset_tag = "2023-02-01T12:00:00Z" + String nextclade_dataset_tag = "2023-02-25T12:00:00Z" String medaka_docker = "quay.io/staphb/artic-ncov2019:1.3.0-medaka-1.4.3" String? nextclade_dataset_name File? reference_genome diff --git a/workflows/wf_theiacov_fasta.wdl b/workflows/wf_theiacov_fasta.wdl index 22c58c2f..e2b61561 100644 --- a/workflows/wf_theiacov_fasta.wdl +++ b/workflows/wf_theiacov_fasta.wdl @@ -15,7 +15,7 @@ workflow theiacov_fasta { String seq_method String input_assembly_method String nextclade_dataset_reference = "MN908947" - String nextclade_dataset_tag = "2023-02-01T12:00:00Z" + String nextclade_dataset_tag = "2023-02-25T12:00:00Z" String? nextclade_dataset_name String organism = "sars-cov-2" } diff --git a/workflows/wf_theiacov_illumina_pe.wdl b/workflows/wf_theiacov_illumina_pe.wdl index a1c153da..2c7941f1 100644 --- a/workflows/wf_theiacov_illumina_pe.wdl +++ b/workflows/wf_theiacov_illumina_pe.wdl @@ -25,7 +25,7 @@ workflow theiacov_illumina_pe { File read2_raw File? primer_bed String nextclade_dataset_reference = "MN908947" - String nextclade_dataset_tag = "2023-02-01T12:00:00Z" + String nextclade_dataset_tag = "2023-02-25T12:00:00Z" String? nextclade_dataset_name File? reference_gff File? reference_genome diff --git a/workflows/wf_theiacov_illumina_se.wdl b/workflows/wf_theiacov_illumina_se.wdl index 2216d1da..074f6c9a 100644 --- a/workflows/wf_theiacov_illumina_se.wdl +++ b/workflows/wf_theiacov_illumina_se.wdl @@ -21,7 +21,7 @@ workflow theiacov_illumina_se { File read1_raw File? primer_bed String nextclade_dataset_reference = "MN908947" - String nextclade_dataset_tag = "2023-02-01T12:00:00Z" + String nextclade_dataset_tag = "2023-02-25T12:00:00Z" String? nextclade_dataset_name File? reference_genome Int min_depth = 100 diff --git a/workflows/wf_theiacov_ont.wdl b/workflows/wf_theiacov_ont.wdl index a5f40d51..324489dd 100644 --- a/workflows/wf_theiacov_ont.wdl +++ b/workflows/wf_theiacov_ont.wdl @@ -23,7 +23,7 @@ workflow theiacov_ont { File demultiplexed_reads Int normalise = 200 String nextclade_dataset_reference = "MN908947" - String nextclade_dataset_tag = "2023-02-01T12:00:00Z" + String nextclade_dataset_tag = "2023-02-25T12:00:00Z" String? nextclade_dataset_name File? reference_genome Int max_length = 700