Merge resolution

.gitlab-ci.yml

 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/

CHANGELOG.md

+# 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

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>

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'
   }

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 {

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'
 }