update CI. also removed 'defaults' from conda channels used to instal…

…l/setup CI env. hopefully that doesn't break everything
theiagen · Oct 29, 2024 · e13b381 · e13b381
1 parent e9bbe00
commit e13b381
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Showing 3 changed files with 5 additions and 9 deletions.
diff --git 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
@@ -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
@@ -416,22 +416,21 @@
     - 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
       md5sum: 5fcafec683df465a99878ceaffe8a294
     - 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