diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 34062a6bedaf41b7d145f2556276cb8d425ddbb1..f9a5b7b8b017f73d5f0f86efb4684f1ff2ba930e 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -1,6 +1,6 @@ before_script: - module load python/3.6.4-anaconda - - pip install --user attrs==19.1.0 pytest-pythonpath==0.7.1 pytest-cov==2.5.1 deriva==1.3.0 + - pip install --user attrs==19.1.0 pytest-pythonpath==0.7.1 pytest-cov==2.5.1 - module load singularity/3.5.3 - module load nextflow/20.01.0 - ln -sfn /project/BICF/BICF_Core/shared/gudmap/test_data/* ./test_data/ diff --git a/CHANGELOG.md b/CHANGELOG.md index 025eec05f1490b1c1d2a7a786c7611228e38f1d6..d291ce8ff00500d597cff6db858ce18e0664aa19 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,30 @@ +# v1.0.2 +**User Facing** + +**Background** +* Fix spelling in config file for process of failed fastq to upload error message (#104) + +*Known Bugs* +* Override params (inputBag, fastq, species) aren't checked for integrity +* Authentication files and tokens must be active (active auth client) for the duration of the pipeline run (until long-lived token utilization included) + +<hr> + +# v1.0.1 +**User Facing** + +**Background** +* Split non-metadata mismatch error handling proces into 2, 1 to handle fastq errors and one for species errors (BUG FIX #101) +* Add known errors to integration CI tests (ambiguous species, trunkated fastq, R1/R2 mismatch (#103) +* Fix pre exeuction run fails uploading of execution run RID to tracking site (#96, #97) +* Change CI replicate count badge CI to count all execution runs that match major version + +*Known Bugs* +* Override params (inputBag, fastq, species) aren't checked for integrity +* Authentication files and tokens must be active (active auth client) for the duration of the pipeline run (until long-lived token utilization included) + +<hr> + # v1.0.0 **User Facing** * Add link to reference builder script diff --git a/docs/software_versions_mqc.yaml b/docs/software_versions_mqc.yaml index b1982d393f7f24cf549a830d48be20afc749533b..5eb233d1b251787f3ad3cd14b2b7133259383e02 100755 --- a/docs/software_versions_mqc.yaml +++ b/docs/software_versions_mqc.yaml @@ -20,5 +20,5 @@ <dt>deepTools</dt><dd>v3.5.0</dd> <dt>FastQC</dt><dd>v0.11.9</dd> <dt>MultiQC</dt><dd>v1.9</dd> - <dt>Pipeline Version</dt><dd>v1.0.1</dd> + <dt>Pipeline Version</dt><dd>v1.0.2</dd> </dl> diff --git a/workflow/conf/aws.config b/workflow/conf/aws.config index cdd91da7bb7ede67aa9a004ab4d617186edee334..eec8a7a829280d29006d9f0dc9f9b9932d9a9867 100644 --- a/workflow/conf/aws.config +++ b/workflow/conf/aws.config @@ -112,7 +112,12 @@ process { cpus = 1 memory = '1 GB' } - withName:failPreExecutionRun { + withName:failPreExecutionRun_fastq { + cpus = 1 + memory = '1 GB' + } + withName:failPreExecutionRun_species { + { cpus = 1 memory = '1 GB' } diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config index 8cfc34ad4e8deea2735e0e49f613dfa48bb6defc..33917dbe810969bc6de2482dba00df16b06547ce 100755 --- a/workflow/conf/biohpc.config +++ b/workflow/conf/biohpc.config @@ -82,10 +82,10 @@ process { withName:finalizeExecutionRun { executor = 'local' } - withName:failPreExecutionRun { + withName:failPreExecutionRun_fastq { executor = 'local' } - withName:failPreExecutionRun { + withName:failPreExecutionRun_species { executor = 'local' } withName:failExecutionRun { diff --git a/workflow/nextflow.config b/workflow/nextflow.config index 8d23a6c8136bcc357afc54a1626f69ad50eeb805..66b847beffb6499b9ba16678887ed0488c2d12cb 100644 --- a/workflow/nextflow.config +++ b/workflow/nextflow.config @@ -88,7 +88,10 @@ process { withName:finalizeExecutionRun { container = 'gudmaprbk/deriva1.4:1.0.0' } - withName:failPreExecutionRun { + withName:failPreExecutionRun_fastq { + container = 'gudmaprbk/deriva1.4:1.0.0' + } + withName:failPreExecutionRun_species { container = 'gudmaprbk/deriva1.4:1.0.0' } withName:failExecutionRun { @@ -122,6 +125,6 @@ manifest { homePage = 'https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq' description = 'This pipeline was created to be a standard mRNA-sequencing analysis pipeline which integrates with the GUDMAP and RBK consortium data-hub.' mainScript = 'rna-seq.nf' - version = 'v1.0.1' + version = 'v1.0.2' nextflowVersion = '>=19.09.0' }