From e13b381aa6b798a2240430877326c0410d2008e8 Mon Sep 17 00:00:00 2001 From: Curtis Kapsak Date: Tue, 29 Oct 2024 18:41:57 +0000 Subject: [PATCH] update CI. also removed 'defaults' from conda channels used to install/setup CI env. hopefully that doesn't break everything --- tests/config/environment.yml | 1 - tests/workflows/theiacov/test_wf_theiacov_illumina_pe.yml | 5 ++--- .../workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml | 8 +++----- 3 files changed, 5 insertions(+), 9 deletions(-) diff --git a/tests/config/environment.yml b/tests/config/environment.yml index 0aed07151..c4016d3ae 100644 --- a/tests/config/environment.yml +++ b/tests/config/environment.yml @@ -2,7 +2,6 @@ name: pytest-env-CI channels: - conda-forge - bioconda - - defaults dependencies: - python >=3.7 - cromwell=86 diff --git a/tests/workflows/theiacov/test_wf_theiacov_illumina_pe.yml b/tests/workflows/theiacov/test_wf_theiacov_illumina_pe.yml index 4c7542334..5b5d2d2d0 100644 --- a/tests/workflows/theiacov/test_wf_theiacov_illumina_pe.yml +++ b/tests/workflows/theiacov/test_wf_theiacov_illumina_pe.yml @@ -60,11 +60,11 @@ md5sum: d41d8cd98f00b204e9800998ecf8427e # fastq scan raw - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/command - md5sum: 9b2cc0107f1a90972482d7b3a658d242 + md5sum: 56bcc1ba5d2a9c94f4704fc4b8e6b7ba - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/inputs.json contains: ["read1", "read2", "illumina_pe"] - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/outputs.json - contains: ["fastq_scan_pe", "pipeline_date", "read1_seq", "read2_seq"] + contains: ["fastq_scan_pe", "read1_seq", "read2_seq"] - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/stderr.txt - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/stderr.txt.offset - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/stdout.txt @@ -74,7 +74,6 @@ md5sum: 2a77387b247176aa5fcc9aed228699c9 - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/SRR13687078_2_fastq-scan.json md5sum: d0eebdd4e14cf0a0b371fee1338474c9 - - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/DATE - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/READ1_SEQS md5sum: 4e4a08422dbf7001fd09ad5126e13b44 - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/READ2_SEQS diff --git a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml index 71f5bd4a2..6f28552fe 100644 --- a/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml +++ b/tests/workflows/theiaprok/test_wf_theiaprok_illumina_pe.yml @@ -416,14 +416,13 @@ - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/inputs.json contains: ["read", "fastq"] - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/outputs.json - contains: ["read", "fastq", "fastq_scan_report"] + contains: ["read", "fastq", "fastq_scan_json"] - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/stderr.txt - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/stderr.txt.offset - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/stdout.txt contains: ["fastq", "qc_stats", "read_lengths"] - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/task.log contains: ["wdl", "theiaprok_illumina_pe", "fastq_scan_clean", "done"] - - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/DATE - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/READ1_SEQS md5sum: 5fcafec683df465a99878ceaffe8a294 - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/READ2_SEQS @@ -431,7 +430,7 @@ - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/READ_PAIRS md5sum: 5fcafec683df465a99878ceaffe8a294 - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/VERSION - md5sum: 8e4e9cdfbacc9021a3175ccbbbde002b + md5sum: a59bb42644e35c09b8fa8087156fa4c2 - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/_miniwdl_inputs/0/test_1.clean.fastq.gz - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/_miniwdl_inputs/0/test_2.clean.fastq.gz - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_clean/work/test_1.clean_fastq-scan.json @@ -450,7 +449,6 @@ contains: ["fastq", "qc_stats", "read_lengths"] - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/task.log contains: ["wdl", "theiaprok_illumina_pe", "fastq_scan_raw", "done"] - - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/DATE - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/READ1_SEQS md5sum: 75fa2f47fecb5dec8d244366881e76ec - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/READ2_SEQS @@ -462,7 +460,7 @@ - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/SRR2838702_R2_fastq-scan.json md5sum: e81f34050c11995771de79182f06d793 - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/VERSION - md5sum: 8e4e9cdfbacc9021a3175ccbbbde002b + md5sum: a59bb42644e35c09b8fa8087156fa4c2 - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/_miniwdl_inputs/0/SRR2838702_R1.fastq.gz - path: miniwdl_run/call-read_QC_trim/call-fastq_scan_raw/work/_miniwdl_inputs/0/SRR2838702_R2.fastq.gz - path: miniwdl_run/call-read_QC_trim/call-trimmomatic_pe/command