diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 14426c66432381603b332f05c340e0a7591c4cf4..21b094892729ce9518c6b74ec6cab0979a436aa3 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -183,7 +183,7 @@ getBag:
     - derivaVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deriva | cut -d"/" -f2 | cut -d":" -f2)
     - echo ${dir}${derivaImg}_${derivaVar}.sif
     - ln -sfn `readlink -e ./test_data/auth/credential.json` ~/.deriva/credential.json
-    - singularity run ${dir}${derivaImg}_${derivaVar}.sif deriva-download-cli staging.gudmap.org --catalog 2 ./workflow/conf/Replicate_For_Input_Bag.json . rid=Q-Y5F6
+    - singularity run ${dir}${derivaImg}_${derivaVar}.sif deriva-download-cli staging.gudmap.org --catalog 2 ./workflow/conf/Replicate_For_Input_Bag.json . rid=${ci_staging_rid_rep}
     - pytest -m getBag
 
 getData:
@@ -197,7 +197,7 @@ getData:
   script:
     - derivaImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deriva | cut -d"/" -f2 | cut -d":" -f1)
     - derivaVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deriva | cut -d"/" -f2 | cut -d":" -f2)
-    -  echo ${dir}${derivaImg}_${derivaVar}.sif
+    - echo ${dir}${derivaImg}_${derivaVar}.sif
     - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
     - unzip ./test_data/bag/Q-Y5F6_inputBag_xxxxtest.zip
     - singularity run ${dir}${derivaImg}_${derivaVar}.sif bash ./workflow/scripts/bdbag_fetch.sh Q-Y5F6_inputBag Q-Y5F6
@@ -255,7 +255,7 @@ seqwho:
     - seqwhoImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqwho | cut -d"/" -f2 | cut -d":" -f1)
     - seqwhoVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep seqwho | cut -d"/" -f2 | cut -d":" -f2)
     - echo ${dir}${seqwhoImg}_${seqwhoVar}.sif
-    - wget -O SeqWho.ix https://cloud.biohpc.swmed.edu/index.php/s/eeNWqZz8jqN5zWY/download
+    - wget -O SeqWho.ix https://cloud.biohpc.swmed.edu/index.php/s/sP48taKmymSkJBM/download
     - mkdir -p SeqWho_call_plots/test_data/fastq/small/
     - singularity run ${dir}${seqwhoImg}_${seqwhoVar}.sif seqwho.py -f test_data/fastq/small/Q-Y5F6_1M.R1.fastq.gz -x SeqWho.ix
     - pytest -m seqwho
@@ -452,16 +452,16 @@ uploadExecutionRun:
     - echo ${dir}${derivaImg}_${derivaVar}.sif
     - ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
     - >
-      exist=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Execution_Run/Replicate=17-BTFJ) &&
+      exist=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Execution_Run/Replicate=${ci_staging_rid_test_rep}) &&
       cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
       cookie=${cookie:11:-1} &&
       if [ "${exist}" == "[]" ]; then
-        rid=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif python3 ./workflow/scripts/upload_execution_run.py -r 17-BTFJ -w 17-BV2Y -g 17-BV90 -i 17-BTFT -s Success -d 'This is a test execution run' -o staging.gudmap.org -c ${cookie} -u F) &&
+        rid=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif python3 ./workflow/scripts/upload_execution_run.py -r ${ci_staging_rid_test_rep} -w ${ci_staging_rid_wf} -g ${ci_staging_rid_genome} -i ${ci_staging_rid_test_ibag} -s Success -d 'This is a test execution run' -o staging.gudmap.org -c ${cookie} -u F) &&
         echo ${rid} test execution run created
       else
         rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') &&
         rid=${rid:7:-6} &&
-        rid=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif python3 ./workflow/scripts/upload_execution_run.py -r 17-BTFJ -w 17-BV2Y -g 17-BV90 -i 17-BTFT -s Success -d 'This is a test execution run' -o staging.gudmap.org -c ${cookie} -u ${rid}) &&
+        rid=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif python3 ./workflow/scripts/upload_execution_run.py -r ${ci_staging_rid_test_rep} -w ${ci_staging_rid_wf} -g ${ci_staging_rid_genome} -i ${ci_staging_rid_test_ibag} -s Success -d 'This is a test execution run' -o staging.gudmap.org -c ${cookie} -u ${rid}) &&
         echo ${rid} test execution run already exists
       fi
 
@@ -479,7 +479,7 @@ uploadQC:
     - echo ${dir}${derivaImg}_${derivaVar}.sif
     - ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
     - >
-      exist=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:mRNA_QC/Replicate=17-BTFJ) &&
+      exist=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:mRNA_QC/Replicate=${ci_staging_rid_test_rep}) &&
       cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
       cookie=${cookie:11:-1} &&
       if [ "${exist}" != "[]" ]; then
@@ -489,7 +489,7 @@ uploadQC:
         done
         echo all old mRNA QC RIDs deleted
       fi
-        rid=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif python3 ./workflow/scripts/upload_qc.py -r 17-BTFJ -e 17-BVDJ -p "Single End" -s forward -l 35 -w 5 -f 1 -t 1 -n "This is a test mRNA QC" -o staging.gudmap.org -c ${cookie} -u F)
+        rid=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif python3 ./workflow/scripts/upload_qc.py -r ${ci_staging_rid_test_rep} -e ${ci_staging_rid_test_erun} -p "Single End" -s forward -l 35 -w 5 -f 1 -t 1 -n "This is a test mRNA QC" -o staging.gudmap.org -c ${cookie} -u F)
         echo ${rid} test mRNA QC created
 
 uploadProcessedFile:
@@ -505,11 +505,11 @@ uploadProcessedFile:
     - derivaVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep deriva | cut -d"/" -f2 | cut -d":" -f2)
     - echo ${dir}${derivaImg}_${derivaVar}.sif
     - ln -sfn `readlink -e ./test_data/auth/credential.json` ./credential.json
-    - echo THIS IS A TEST FILE > 17-BTFJ_test.csv
-    - mkdir -p ./deriva/Seq/pipeline/17-BTFE/17-BVDJ/
-    - mv 17-BTFJ_test.csv ./deriva/Seq/pipeline/17-BTFE/17-BVDJ/17-BTFJ_test.csv
+    - echo THIS IS A TEST FILE > ${ci_staging_rid_test_rep}_test.csv
+    - mkdir -p ./deriva/Seq/pipeline/${ci_staging_rid_test_study}/${ci_staging_rid_test_erun}/
+    - mv ${ci_staging_rid_test_rep}_test.csv ./deriva/Seq/pipeline/${ci_staging_rid_test_study}/${ci_staging_rid_test_erun}/${ci_staging_rid_test_rep}_test.csv
     - >
-      exist=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Processed_File/Replicate=17-BTFJ) &&
+      exist=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif curl -s https://staging.gudmap.org/ermrest/catalog/2/entity/RNASeq:Processed_File/Replicate=${ci_staging_rid_test_rep}) &&
       cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
       cookie=${cookie:11:-1} &&
       if [ "${exist}" != "[]" ]; then
@@ -548,7 +548,7 @@ uploadOutputBag:
         cookie=$(cat credential.json | grep -A 1 '\"staging.gudmap.org\": {' | grep -o '\"cookie\": \".*\"') &&
         cookie=${cookie:11:-1} &&
         loc=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif deriva-hatrac-cli --host staging.gudmap.org put ./test.txt /hatrac/resources/rnaseq/pipeline/output_bag/TEST/test.txt --parents) &&
-        rid=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif python3 ./workflow/scripts/upload_output_bag.py -e 17-BVDJ -f test.txt -l ${loc} -s ${md5} -b ${size} -n 'This is a test output bag' -o staging.gudmap.org -c ${cookie}) &&
+        rid=$(singularity run ${dir}${derivaImg}_${derivaVar}.sif python3 ./workflow/scripts/upload_output_bag.py -e ${ci_staging_rid_test_erun} -f test.txt -l ${loc} -s ${md5} -b ${size} -n 'This is a test output bag' -o staging.gudmap.org -c ${cookie} -u "F") &&
         echo ${rid} test output bag created
       else
         rid=$(echo ${exist} | grep -o '\"RID\":\".*\",\"RCT') &&
@@ -767,7 +767,7 @@ integration_se:
   script:
     - hostname
     - ulimit -a
-    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-1ZX4 --source staging --refSource datahub --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./SE_report.html
+    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-1ZX4 --source staging --refSource datahub --upload true -with-dag dag.png -with-report ./SE_report.html
     - find . -type f -name "multiqc_data.json" -exec cp {} ./SE_multiqc_data.json \;
     - pytest -m completionMultiqc --filename SE_multiqc_data.json
   artifacts:
@@ -792,7 +792,7 @@ integration_pe:
   script:
     - hostname
     - ulimit -a
-    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5JA --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./PE_report.html
+    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5JA --source staging --upload true -with-dag dag.png -with-report ./PE_report.html
     - find . -type f -name "multiqc_data.json" -exec cp {} ./PE_multiqc_data.json \;
     - pytest -m completionMultiqc --filename PE_multiqc_data.json
   artifacts:
@@ -810,81 +810,6 @@ integration_pe:
       - always
 
 
-failTrunkation:
-  stage: integration
-  only: [merge_requests]
-  except:
-    variables:
-      - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
-  script:
-    - hostname
-    - ulimit -a
-    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5ET --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failTrunkation_report.html
-  retry:
-    max: 0
-    when:
-      - always
-
-failMismatchR1R2:
-  stage: integration
-  only: [merge_requests]
-  except:
-    variables:
-      - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
-  script:
-    - hostname
-    - ulimit -a
-    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-CWH4 --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failMismatchR1R2_report.html
-  retry:
-    max: 0
-    when:
-      - always
-
-failUnexpectedMeta:
-  stage: integration
-  only: [merge_requests]
-  except:
-    variables:
-      - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
-  script:
-    - hostname
-    - ulimit -a
-    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 14-3R4R --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failUnexpectedMeta_report.html
-  retry:
-    max: 0
-    when:
-      - always
-
-failFileStructure:
-  stage: integration
-  only: [merge_requests]
-  except:
-    variables:
-      - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
-  script:
-    - hostname
-    - ulimit -a
-    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5HT --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failFileStructure_report.html
-  retry:
-    max: 0
-    when:
-      - always
-
-failSeqType:
-  stage: integration
-  only: [merge_requests]
-  except:
-    variables:
-      - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
-  script:
-    - hostname
-    - ulimit -a
-    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID 16-DNDJ --source staging --upload true -with-dag dag.png --dev false --ci true --track true -with-report ./failSeqType_report.html
-  retry:
-    max: 0
-    when:
-      - always
-
 override_inputBag:
   stage: integration
   only: [merge_requests]
@@ -894,7 +819,7 @@ override_inputBag:
   script:
     - hostname
     - ulimit -a
-    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --source staging --inputBagForce ./test_data/bag/Q-Y5F6_inputBag_xxxxxxxx.zip --upload false --dev false --ci true --track false -with-report ./inputBagOverride_report.html
+    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6 --source staging --inputBagForce ./test_data/bag/Q-Y5F6_inputBag_xxxxxxxx.zip --upload false -with-report ./inputBagOverride_report.html
     - find . -type f -name "multiqc_data.json" -exec cp {} ./inputBagOverride_multiqc_data.json \;
     - find ./**/report/ -type f -name "*multiqc.html" -exec cp {} ./inputBagOverride_multiqc.html \;
     - pytest -m completionMultiqc --filename inputBagOverride_multiqc_data.json
@@ -919,7 +844,7 @@ override_fastq:
   script:
     - hostname
     - ulimit -a
-    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6  --source staging --fastqsForce './test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz' --upload false --dev false --ci true --track false -with-report ./fastqOverride_report.html
+    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F6  --source staging --fastqsForce './test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz' --upload false -with-report ./fastqOverride_report.html
     - find . -type f -name "multiqc_data.json" -exec cp {} ./fastqOverride_multiqc_data.json \;
     - find ./**/report/ -type f -name "*multiqc.html" -exec cp {} ./fastqOverride_multiqc.html \;
     - pytest -m completionMultiqc --filename fastqOverride_multiqc_data.json
@@ -944,7 +869,7 @@ override_species:
   script:
     - hostname
     - ulimit -a
-    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5EW --source staging --speciesForce 'Homo sapiens' --upload true --dev false --ci true --track false -with-report ./speciesOverride_report.html
+    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5EW --source staging --speciesForce 'Homo sapiens' --upload true -with-report ./speciesOverride_report.html
     - find . -type f -name "multiqc_data.json" -exec cp {} ./speciesOverride_multiqc_data.json \;
     - find ./**/report/ -type f -name "*multiqc.html" -exec cp {} ./speciesOverride_multiqc.html \;
     - pytest -m completionMultiqc --filename speciesOverride_multiqc_data.json
@@ -969,7 +894,7 @@ override_stranded:
   script:
     - hostname
     - ulimit -a
-    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5EY --source staging --strandedForce unstranded --upload true --dev false --ci true --track false -with-report ./strandedOverride_report.html
+    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5EY --source staging --strandedForce unstranded --upload true -with-report ./strandedOverride_report.html
     - find . -type f -name "multiqc_data.json" -exec cp {} ./strandedOverride_multiqc_data.json \;
     - find ./**/report/ -type f -name "*multiqc.html" -exec cp {} ./strandedOverride_multiqc.html \;
     - pytest -m completionMultiqc --filename strandedOverride_multiqc_data.json
@@ -994,7 +919,7 @@ override_spike:
   script:
     - hostname
     - ulimit -a
-    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F0 --source staging --spikeForce true --upload true --dev false --ci true --track false -with-report ./spikeOverride_report.html
+    - nextflow -q run ./rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5F0 --source staging --spikeForce true --upload true -with-report ./spikeOverride_report.html
     - find . -type f -name "multiqc_data.json" -exec cp {} ./spikeOverride_multiqc_data.json \;
     - find ./**/report/ -type f -name "*multiqc.html" -exec cp {} ./spikeOverride_multiqc.html \;
     - pytest -m completionMultiqc --filename spikeOverride_multiqc_data.json
@@ -1127,4 +1052,4 @@ aws:
     when: always
     paths:
       - badges/
-  allow_failure: true
\ No newline at end of file
+  allow_failure: true
diff --git a/CHANGELOG.md b/CHANGELOG.md
index a85a844ae1fbdc299eb175ab14449bf9e20d40e0..76ca7d646ddf2ab51c859c7fca459ec710de15b3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,25 @@
+# v.2.0.1 (indev)
+**User Facing**
+* Corrected spelling of inferred (#125)
+ce
+* Add seqtype force parameter (#131)
+* Add param for seqwho reference (#127)
+* Remove tracking param and all tracking code
+
+
+**Background**
+* Corrected file search parameters due to name inconsistency (#129)
+* Re-implemented sym-link for deriva cookie into ~/.bdbag/ for bdbag fetch to use (#132)
+* Add CI variables for staging RIDs (#133)
+* Use CI staging RIDs for CI unit tests: getBag, uploadInputBag, uploadExecutionRun, uploadQC, uploadProcessedFiles, uploadOutputBag (#133)
+* Add `-u "F"` to CI unit test uploadOutputBag `upload_output_bag.py`
+* Remove "fail" integration CI tests (#133 addendum)
+* Add licence header to nf file,  R and python scriptsand pytest scripts
+* Stop using RCB and RMB (default) with deriva.core insert calls to match server update (#134)
+* Replace default seqwho reference location to one provided by source lab (#127)
+* Update NF Tower access token to BICF user
+* Disable NF Tower
+
 # v2.0.0
 **User Facing**
 * Endness metadata "Single Read" changed to "Single End" in data-hub, pipeline updated to handle (#110) ("Single Read" still acceptable for backwards compatibility)
diff --git a/README.md b/README.md
index 7692cb70b453218bcf04ec31dd21ec0fcae7678c..7e5abc805b2f91b1c545b1e79e118585216be5a2 100644
--- a/README.md
+++ b/README.md
@@ -17,7 +17,13 @@ This pipeline was created to be a standard mRNA-sequencing analysis pipeline whi
 
 Authentication:
 ----------------
-The consortium server used must be authentificated with the [deriva authentication client](https://github.com/informatics-isi-edu/gudmap-rbk/wiki/), and remain authentificated till the end of the pipeline run. Prematurely closing the client will result in invalidation of the tokens, and may result in the pipeline failure. The use of long-lived "globus" tokens is on the roadmap for use in the future.
+The consortium server used must be authentificated with the [deriva authentication client](https://github.com/informatics-isi-edu/gudmap-rbk/wiki/), and remain authentificated till the end of the pipeline run. Prematurely closing the client will result in invalidation of the tokens, and may result in the pipeline failure. The use of long-lived "globus" tokens is on the roadmap for use in the future. If you are using [v2.0.0](https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/tags/v2.0.0) you will be required to make a link for bdbag cookie. Below is the code to run:
+
+```sh
+mkdir -p ~/.bdbag
+ln -sf cookies.txt ~/.bdbag/deriva-cookies.txt
+```
+
 
 To Run:
 -------
@@ -32,6 +38,7 @@ To Run:
   * `--refMoVersion` mouse reference version ***(optional, default = 38.p6.vM25)***
   * `--refHuVersion` human reference version ***(optional, default = 38.p13.v36)***
   * `--refERCCVersion` human reference version ***(optional, default = 92)***
+  * `--seqwhoRef` seqwho reference location ***(optional, default = https://cloud.biohpc.swmed.edu/index.php/s/sP48taKmymSkJBM/download)***
   * `--upload` option to not upload output back to the data-hub ***(optional, default = false)***
     * **true** = upload outputs to the data-hub
     * **false** = do *NOT* upload outputs to the data-hub
@@ -57,6 +64,8 @@ To Run:
     * eg: `--inputBagForce test_data/bag/Q-Y5F6_inputBag_xxxxxxxx.zip` (must be the expected bag structure, this example will not work because it is a test bag)
   * `--fastqsForce` utilizes local fastq's instead of downloading from the data-hub (still requires accurate repRID input)
     * eg: `--fastqsForce 'test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz'` (note the quotes around fastq's which must me named in the correct standard [*\*.R1.fastq.gz and/or \*.R2.fastq.gz*] and in the correct order, also consider using `endsForce` if the endness doesn't match submitted value)
+  * `--seqtypeForce` forces the sequencing type to be mRNAseq, it bypasses a inferred mismatch or an ambiguous error
+    * eg: `--seqtypeForce 'mRNAseq'`
   * `--speciesForce` forces the species to be "Mus musculus" or "Homo sapiens", it bypasses a metadata mismatch or an ambiguous species error
     * eg: `--speciesForce 'Mus musculus'`
   * `--endsForce` forces the endness to be "se", or "pe", it bypasses a metadata mismatch error
@@ -65,9 +74,6 @@ To Run:
     * eg: `--strandedForce 'unstranded'`
   * `--spikeForce` forces the spike-in to be "false", or "true", it bypasses a metadata mismatch error
     * eg: `--spikeForce 'true'`
-* Tracking parameters ([Tracking Site](http://bicf.pipeline.tracker.s3-website-us-east-1.amazonaws.com/)):
-  * `--ci` boolean (default = false)
-  * `--dev` boolean (default = true)
 
 FULL EXAMPLE:
 -------------
diff --git a/conf/multiqc_config.yaml b/conf/multiqc_config.yaml
index ed1375aed47a454394029e5057695b0c15babd8c..1484c4dbad62d6aaf6c8d995d02723f8b5ccc15f 100644
--- a/conf/multiqc_config.yaml
+++ b/conf/multiqc_config.yaml
@@ -103,7 +103,7 @@ custom_data:
     meta:
         file_format: 'tsv'
         section_name: 'Metadata'
-        description: 'This is the comparison of infered metadata, submitter provided, and calculated'
+        description: 'This is the comparison of inferred metadata, submitter provided, and calculated'
         plot_type: 'table'
         pconfig:
             id: 'meta'
diff --git a/docs/dag.png b/docs/dag.png
old mode 100755
new mode 100644
index f80f38b64729f19e6c78b29ee2af427eebe4aaba..3687de2ad848fa9785e3ba0abf4f6544eebae45b
Binary files a/docs/dag.png and b/docs/dag.png differ
diff --git a/nextflow.config b/nextflow.config
index fbfb2f154ec529822550560fe2fac158219212e0..03fe237afa8ff00a8b4d5b5f67c3d09efaedad6a 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -110,8 +110,9 @@ process {
 }
 
 tower {
-  accessToken = '3ade8f325d4855434b49aa387421a44c63e3360f'
-  enabled = true
+  accessToken = 'eyJ0aWQiOiAzODIyfS42YWFjOWMwZDM4Mjc1NmY0MGJiY2QxNWRkOTZlYTU4MDlmY2NkZmRj'
+  workspaceId = '84512216752206'
+  enabled = false
 }
 
 manifest {
@@ -119,6 +120,6 @@ 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 = 'v2.0.0'
+  version = 'v2.0.1'
   nextflowVersion = '>=20.01.0'
 }
diff --git a/rna-seq.nf b/rna-seq.nf
index 0adcc63f7b7a1a540b2be56a2e94b86376e617bf..3094d2865cf38a41b30476d66593b8bea015593d 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -1,4 +1,10 @@
 #!/usr/bin/env nextflow
+//rna-seq.nf
+//*
+//* --------------------------------------------------------------------------
+//* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+//* --------------------------------------------------------------------------
+//*
 
 //  ########  ####  ######  ########
 //  ##     ##  ##  ##    ## ##
@@ -17,10 +23,10 @@ params.source = "dev"
 params.refMoVersion = "38.p6.vM25"
 params.refHuVersion = "38.p13.v36"
 params.refERCCVersion = "92"
+params.seqwhoRef = "https://cloud.biohpc.swmed.edu/index.php/s/sP48taKmymSkJBM/download"
 params.outDir = "${baseDir}/output"
 params.upload = false
 params.email = ""
-params.track = false
 
 // Define override input variable
 params.refSource = "biohpc"
@@ -30,10 +36,7 @@ params.endsForce = ""
 params.speciesForce = ""
 params.strandedForce = ""
 params.spikeForce = ""
-
-// Define tracking input variables
-params.ci = false
-params.dev = true
+params.seqtypeForce = ""
 
 // Parse input variables
 deriva = Channel
@@ -61,6 +64,7 @@ repRID = params.repRID
 refMoVersion = params.refMoVersion
 refHuVersion = params.refHuVersion
 refERCCVersion = params.refERCCVersion
+seqwhoRef = params.seqwhoRef
 outDir = params.outDir
 logsDir = "${outDir}/Logs"
 upload = params.upload
@@ -70,6 +74,7 @@ endsForce = params.endsForce
 speciesForce = params.speciesForce
 strandedForce = params.strandedForce
 spikeForce = params.spikeForce
+seqtypeForce = params.seqtypeForce
 email = params.email
 
 // Define fixed files and variables
@@ -115,47 +120,6 @@ script_deleteEntry_uploadQC = Channel.fromPath("${baseDir}/workflow/scripts/dele
 script_deleteEntry_uploadQC_fail = Channel.fromPath("${baseDir}/workflow/scripts/delete_entry.py")
 script_deleteEntry_uploadProcessedFile = Channel.fromPath("${baseDir}/workflow/scripts/delete_entry.py")
 
-/*
- * trackStart: track start of pipeline
- */
-process trackStart {
-  script:
-    """
-    hostname
-    ulimit -a
-
-    curl -H 'Content-Type: application/json' -X PUT -d \
-      '{ \
-        "sessionId": "${workflow.sessionId}", \
-        "pipeline": "gudmap.rbk_rnaseq", \
-        "start": "${workflow.start}", \
-        "repRID": "${repRID}", \
-        "astrocyte": false, \
-        "status": "started", \
-        "nextflowVersion": "${workflow.nextflow.version}", \
-        "pipelineVersion": "${workflow.manifest.version}", \
-        "ci": ${params.ci}, \
-        "dev": ${params.dev} \
-      }' \
-      "https://xku43pcwnf.execute-api.us-east-1.amazonaws.com/ProdDeploy/pipeline-tracking"
-
-    if [ ${params.track} == true ]
-    then
-      curl -H 'Content-Type: application/json' -X PUT -d \
-        '{ \
-          "ID": "${workflow.sessionId}", \
-          "repRID": "${repRID}", \
-          "PipelineVersion": "${workflow.manifest.version}", \
-          "Server": "${params.source}", \
-          "Queued": "NA", \
-          "CheckedOut": "NA", \
-          "Started": "${workflow.start}" \
-        }' \
-        "https://9ouc12dkwb.execute-api.us-east-2.amazonaws.com/prod/db/track"
-    fi
-    """
-}
-
 log.info """\
 ====================================
 BICF RNA-seq Pipeline for GUDMAP/RBK
@@ -168,15 +132,11 @@ ERCC Reference Version : ${params.refERCCVersion}
 Reference source       : ${params.refSource}
 Output Directory       : ${params.outDir}
 Upload                 : ${upload}
-Track                  : ${params.track}
 ------------------------------------
 Nextflow Version       : ${workflow.nextflow.version}
 Pipeline Version       : ${workflow.manifest.version}
 Session ID             : ${workflow.sessionId}
 ------------------------------------
-CI                     : ${params.ci}
-Development            : ${params.dev}
-------------------------------------
 """
 
 /*
@@ -206,7 +166,7 @@ process getBag {
     mkdir -p ~/.deriva
     ln -sf `readlink -e credential.json` ~/.deriva/credential.json
     echo -e "LOG: linked" >> ${repRID}.getBag.log
-
+    
     # deriva-download replicate RID
     echo -e "LOG: fetching bag for ${repRID} in GUDMAP" >> ${repRID}.getBag.log
     deriva-download-cli ${source} --catalog 2 ${replicateExportConfig} . rid=${repRID}
@@ -220,7 +180,7 @@ process getBag {
     """
 }
 
-// Set inputBag to downloaded or forced input and replicate them for multiple process inputs 
+// Set inputBag to downloaded or forced input and replicate them for multiple process inputs
 if (inputBagForce != "") {
   inputBag = Channel
     .fromPath(inputBagForce)
@@ -257,6 +217,13 @@ process getData {
     hostname > ${repRID}.getData.log
     ulimit -a >> ${repRID}.getData.log
 
+    # link deriva cookie for authentication
+    echo -e "LOG: linking deriva cookie" >> ${repRID}.getData.log
+    mkdir -p ~/.bdbag
+    ln -sf `readlink -e deriva-cookies.txt` ~/.bdbag/deriva-cookies.txt
+    echo -e "LOG: linked" >> ${repRID}.getData.log
+
+
     # get bag basename
     replicate=\$(basename "${inputBag}")
     echo -e "LOG: bag replicate name \${replicate}" >> ${repRID}.getData.log
@@ -634,7 +601,7 @@ process fastqc {
     # run fastqc
     echo -e "LOG: running fastq on raw fastqs" >> ${repRID}.fastqc.log
     fastqc *.fastq.gz -o . &> fastqc.out || true
-    fastqcErrorOut=\$(cat fastqc.out | grep -c 'Failed to process file') || fastqcErrorOut=0
+    fastqcErrorOut=\$(cat fastqc.out | grep -c 'Failed to process') || fastqcErrorOut=0
     fastqFileError=false
     fastqFileError_details=""
     if [ "\${fastqcErrorOut}" -ne "0" ]
@@ -701,6 +668,7 @@ process seqwho {
   tag "${repRID}"
 
   input:
+    val seqwhoRef
     path (fastq) from fastqs_seqwho
     val ends from endsManual_seqwho
     val speciesMeta from speciesMeta_seqwho
@@ -721,9 +689,9 @@ process seqwho {
     ulimit -a >> ${repRID}.seqwho.log
 
     # get seqwho index
-    wget -O SeqWho.ix https://cloud.biohpc.swmed.edu/index.php/s/eeNWqZz8jqN5zWY/download
+    wget -O SeqWho.ix ${seqwhoRef}
     echo -e "LOG: seqwho index downloaded" >> ${repRID}.seqwho.log
-    
+
     # run seqwho
     seqwho.py -f *.fastq.gz -x SeqWho.ix
     echo -e "LOG: seqwho ran" >> ${repRID}.seqwho.log
@@ -812,7 +780,7 @@ process seqwho {
       echo -e "LOG: concordant species inference: \${speciesInfer}" >> ${repRID}.seqwho.log
     else
       speciesErrorSeqwho=true
-      speciesErrorSeqwho_details="**Infered species does not match for R1 and R2:** Infered R1 = \${speciesR1} and infered R2 = \${speciesR2}"
+      speciesErrorSeqwho_details="**Inferred species does not match for R1 and R2:** Inferred R1 = \${speciesR1} and Inferred R2 = \${speciesR2}"
       echo -e "LOG: inference error: \${speciesErrorSeqwho_details}" >> ${repRID}.seqwho.log
     fi
 
@@ -822,8 +790,8 @@ process seqwho {
       echo -e "LOG: high confidence species inference detected" >> ${repRID}.seqwho.log
     else
       speciesErrorSeqwho=true
-      speciesErrorSeqwho_details=\$(echo "**Infered species confidence is low:**\\n")
-      speciesErrorSeqwho_details=\$(echo \${speciesErrorSeqwho_details}"|fastq|Infered species confidence|\\n")
+      speciesErrorSeqwho_details=\$(echo "**Inferred species confidence is low:**\\n")
+      speciesErrorSeqwho_details=\$(echo \${speciesErrorSeqwho_details}"|fastq|Inferred species confidence|\\n")
       speciesErrorSeqwho_details=\$(echo \${speciesErrorSeqwho_details}"|:--|:--:|\\n")
       speciesErrorSeqwho_details=\$(echo \${speciesErrorSeqwho_details}"|Read 1|\${speciesConfidenceR1}|\\n")
       if [ "${ends}" == "pe" ]
@@ -846,12 +814,12 @@ process seqwho {
           echo -e "LOG: concordant rnaseq seq type inference detected" >> ${repRID}.seqwho.log
         else
           seqtypeError=true
-          seqtypeError_details="**Infered sequencing type is not mRNA-seq:** Infered = \${seqtypeR1}"
+          seqtypeError_details="**Inferred sequencing type is not mRNA-seq:** Inferred = \${seqtypeR1}"
           echo -e "LOG: inference error: \${seqtypeError_details}" >> ${repRID}.seqwho.log
         fi
       else
         seqtypeError=true
-        seqtypeError_details="**Infered sequencing type does not match for R1 and R2:** Infered R1 = \${seqtypeR1} and infered R2 = \${seqtypeR2}"
+        seqtypeError_details="**Inferred sequencing type does not match for R1 and R2:** Inferred R1 = \${seqtypeR1} and Inferred R2 = \${seqtypeR2}"
         echo -e "LOG: inference error: \${seqtypeError_details}" >> ${repRID}.seqwho.log
       fi
       consensus="-"
@@ -901,8 +869,8 @@ process seqwho {
       if [ \${consensus} == false ]
       then
         seqtypeError=true
-        seqtypeError_details=\$(echo "**Infered sequence-type confidence is low:**\\n")
-        seqtypeError_details=\$(echo \${seqtypeError_details}"|fastq|Infered seq type|Infered seq type confidence|\\n")
+        seqtypeError_details=\$(echo "**Inferred sequence-type confidence is low:**\\n")
+        seqtypeError_details=\$(echo \${seqtypeError_details}"|fastq|Inferred seq type|Inferred seq type confidence|\\n")
         seqtypeError_details=\$(echo \${seqtypeError_details}"|:--|:--:|:--:|\\n")
         seqtypeError_details=\$(echo \${seqtypeError_details}"|Read 1|\${seqtypeR1}|\${seqtypeConfidenceR1}|\\n")
         if [ "${ends}" == "pe" ]
@@ -913,6 +881,14 @@ process seqwho {
       fi
     fi
 
+    # override seqtype if forced
+    if [ "${params.seqtypeForce}" == "mRNAseq" ]
+    then
+      seqtypeError=false
+      seqtypeError_details=""
+      echo -e "LOG: seqtype Inferred R1=\${seqtypeR1}; Inferred R2=\${seqtypeR2}; Forced=mRNAseq" >> ${repRID}.seqwho.log
+    fi
+
     # check for species match error
     if [ "${speciesMeta}" != "\${speciesInfer}" ]
     then
@@ -936,7 +912,7 @@ process seqwho {
     then
       echo -e "Read 2\t\${seqtypeR2}\t\${speciesR2}\t\${seqtypeConfidenceR2}\t\${consensus}\t\${speciesConfidenceR2}" >> seqwhoInfer.tsv
     fi
-    
+
     # save species file
     echo "\${speciesInfer}" > inferSpecies.csv
 
@@ -945,7 +921,7 @@ process seqwho {
     """
 }
 
-// Extract infered sepecies metadata into channel and replicate them for multiple process inputs
+// Extract inferred sepecies metadata into channel and replicate them for multiple process inputs
 speciesInfer = Channel.create()
 speciesInfer_failPreExecutionRun = Channel.create()
 inferSpecies_fl.splitCsv(sep: ",", header: false).separate(
@@ -1581,7 +1557,7 @@ strandedInfer.into {
   strandedInfer_failExecutionRun
 }
 
-/* 
+/*
  * checkMetadata: checks the submitted metadata against inferred
  */
 process checkMetadata {
@@ -2104,7 +2080,7 @@ process aggrQC {
     ulimit -a >> ${repRID}.aggrQC.log
 
     # make run table
-    if [ "${params.inputBagForce}" == "" ] && [ "${params.fastqsForce}" == "" ] && [ "${params.speciesForce}" == "" ] && [ "${params.strandedForce}" == "" ] && [ "${params.spikeForce}" == "" ]
+    if [ "${params.inputBagForce}" == "" ] && [ "${params.fastqsForce}" == "" ] && [ "${params.seqtypeForce}" == "" ] && [ "${params.speciesForce}" == "" ] && [ "${params.strandedForce}" == "" ] && [ "${params.spikeForce}" == "" ]
     then
       input="default"
     else
@@ -2117,6 +2093,10 @@ process aggrQC {
       then
         input=\$(echo \${input} fastq)
       fi
+      if [ "${params.seqtypeForce}" == "mRNAseq" ]
+      then
+        input=\$(echo \${input} seqtype)
+      fi
       if [ "${params.speciesForce}" != "" ]
       then
         input=\$(echo \${input} species)
@@ -2182,17 +2162,10 @@ process aggrQC {
     echo -e "LOG: running multiqc" >> ${repRID}.aggrQC.log
     multiqc -c ${multiqcConfig} . -n ${repRID}.multiqc.html
     cp ${repRID}.multiqc_data/multiqc_data.json ${repRID}.multiqc_data.json
-
-    if [ ${params.track} == true ]
-    then
-      curl -H 'Content-Type: application/json' -X PUT -d \
-        @./${repRID}.multiqc_data.json \
-        "https://9ouc12dkwb.execute-api.us-east-2.amazonaws.com/prod/db/qc"
-    fi
     """
 }
 
-/* 
+/*
  * uploadInputBag: uploads the input bag
  */
 process uploadInputBag {
@@ -2230,7 +2203,7 @@ process uploadInputBag {
     echo LOG: ${repRID} input bag md5 sum - \${md5} >> ${repRID}.uploadInputBag.log
     size=\$(wc -c < ./\${file})
     echo LOG: ${repRID} input bag size - \${size} bytes >> ${repRID}.uploadInputBag.log
-    
+
     exist=\$(curl -s https://${source}/ermrest/catalog/2/entity/RNASeq:Input_Bag/File_MD5=\${md5})
     if [ "\${exist}" == "[]" ]
     then
@@ -2265,7 +2238,7 @@ inputBagRID.into {
   inputBagRID_failExecutionRun
 }
 
-/* 
+/*
  * uploadExecutionRun: uploads the execution run
  */
 process uploadExecutionRun {
@@ -2283,7 +2256,7 @@ process uploadExecutionRun {
     val seqtypeError from seqtypeError_uploadExecutionRun
     val speciesErrorSeqwho from speciesErrorSeqwho_uploadExecutionRun
     val speciesError from speciesError_uploadExecutionRun
-    
+
   output:
     path ("executionRunRID.csv") into executionRunRID_fl
 
@@ -2343,16 +2316,6 @@ process uploadExecutionRun {
     fi
 
     echo "\${executionRun_rid}" > executionRunRID.csv
-
-    if [ ${params.track} == true ]
-    then
-      curl -H 'Content-Type: application/json' -X PUT -d \
-        '{ \
-          "ID": "${workflow.sessionId}", \
-          "ExecutionRunRID": "'\${executionRun_rid}'" \
-        }' \
-        "https://9ouc12dkwb.execute-api.us-east-2.amazonaws.com/prod/db/track"
-    fi
     """
 }
 
@@ -2370,7 +2333,7 @@ executionRunRID.into {
   executionRunRID_fail
 }
 
-/* 
+/*
  * uploadQC: uploads the mRNA QC
  */
 process uploadQC {
@@ -2480,7 +2443,7 @@ process uploadProcessedFile {
 
   script:
     """
-    
+
     hostname > ${repRID}.uploadProcessedFile.log
     ulimit -a >> ${repRID}.uploadProcessedFile.log
 
@@ -2550,7 +2513,7 @@ process uploadProcessedFile {
     """
 }
 
-/* 
+/*
  * uploadOutputBag: uploads the output bag
  */
 process uploadOutputBag {
@@ -2597,7 +2560,7 @@ process uploadOutputBag {
     echo LOG: ${repRID} output bag md5 sum - \${md5} >> ${repRID}.uploadOutputBag.log
     size=\$(wc -c < ./\${file})
     echo LOG: ${repRID} output bag size - \${size} bytes >> ${repRID}.uploadOutputBag.log
-    
+
     loc=\$(deriva-hatrac-cli --host ${source} put ./\${file} /hatrac/resources/rnaseq/pipeline/output_bag/study/${studyRID}/replicate/${repRID}/\${file} --parents)
     echo LOG: output bag uploaded - \${loc} >> ${repRID}.uploadOutputBag.log
     # url-ify the location
@@ -2632,7 +2595,7 @@ outputBagRID_fl.splitCsv(sep: ",", header: false).separate(
   outputBagRID
 )
 
-/* 
+/*
  * finalizeExecutionRun: finalizes the execution run
  */
 process finalizeExecutionRun {
@@ -2670,17 +2633,6 @@ process finalizeExecutionRun {
 
     rid=\$(python3 ${script_uploadExecutionRun_finalizeExecutionRun} -r ${repRID} -w \${workflow} -g \${genome} -i ${inputBagRID} -s Success -d 'Run Successful' -o ${source} -c \${cookie} -u ${executionRunRID})
     echo LOG: execution run RID marked as successful - \${rid} >> ${repRID}.finalizeExecutionRun.log
-
-    if [ ${params.track} == true ]
-    then
-    dt=`date +%FT%T.%3N%:z`
-      curl -H 'Content-Type: application/json' -X PUT -d \
-        '{ \
-          "ID": "${workflow.sessionId}", \
-          "Complete": "'\${dt}'" \
-        }' \
-        "https://9ouc12dkwb.execute-api.us-east-2.amazonaws.com/prod/db/track"
-    fi
     """
 }
 
@@ -2698,7 +2650,7 @@ errorDetails.into {
 }
 
 
-/* 
+/*
  * failPreExecutionRun: fail the execution run prematurely for fastq errors
  */
 process failPreExecutionRun {
@@ -2778,18 +2730,6 @@ process failPreExecutionRun {
     fi
 
     echo "\${rid}" > executionRunRID.csv
-
-    if [ ${params.track} == true ]
-    then
-    dt=`date +%FT%T.%3N%:z`
-      curl -H 'Content-Type: application/json' -X PUT -d \
-        '{ \
-          "ID": "${workflow.sessionId}", \
-          "ExecutionRunRID": "'\${rid}'", \
-          "Failure": "'\${dt}'" \
-        }' \
-        "https://9ouc12dkwb.execute-api.us-east-2.amazonaws.com/prod/db/track"
-    fi
   """
 }
 // Extract execution run RID into channel
@@ -2798,7 +2738,7 @@ executionRunRID_preFail_fl.splitCsv(sep: ",", header: false).separate(
   executionRunRID_preFail
 )
 
-/* 
+/*
  * failPreExecutionRun_seqwho: fail the execution run prematurely for seqwho errors
  */
 process failPreExecutionRun_seqwho {
@@ -2879,18 +2819,6 @@ process failPreExecutionRun_seqwho {
     fi
 
     echo "\${rid}" > executionRunRID.csv
-
-    if [ ${params.track} == true ]
-    then
-    dt=`date +%FT%T.%3N%:z`
-      curl -H 'Content-Type: application/json' -X PUT -d \
-        '{ \
-          "ID": "${workflow.sessionId}", \
-          "ExecutionRunRID": "'\${rid}'", \
-          "Failure": "'\${dt}'" \
-        }' \
-        "https://9ouc12dkwb.execute-api.us-east-2.amazonaws.com/prod/db/track"
-    fi
   """
 }
 // Extract execution run RID into channel
@@ -2902,7 +2830,7 @@ executionRunRID_preFailseqwho_fl.splitCsv(sep: ",", header: false).separate(
 
 failExecutionRunRID = executionRunRID_fail.ifEmpty('').mix(executionRunRID_preFail.ifEmpty('').mix(executionRunRID_preFailseqwho.ifEmpty(''))).filter { it != "" }
 
-/* 
+/*
  * failExecutionRun: fail the execution run
  */
 process failExecutionRun {
@@ -2982,22 +2910,10 @@ process failExecutionRun {
       rid=\$(python3 ${script_uploadExecutionRun_failExecutionRun} -r ${repRID} -w \${workflow} -g \${genome} -i ${inputBagRID} -s Error -d "\${pipelineError_details}" -o ${source} -c \${cookie} -u ${executionRunRID})
       echo LOG: execution run RID marked as error - \${rid} >> ${repRID}.failExecutionRun.log
     fi
-    
-    if [ ${params.track} == true ]
-    then
-      dt=`date +%FT%T.%3N%:z`
-      curl -H 'Content-Type: application/json' -X PUT -d \
-        '{ \
-          "ID": "${workflow.sessionId}", \
-          "ExecutionRunRID": "'\${rid}'", \
-          "Failure": "'\${dt}'" \
-        }' \
-        "https://9ouc12dkwb.execute-api.us-east-2.amazonaws.com/prod/db/track"
-    fi
   """
 }
 
-/* 
+/*
  * uploadQC_fail: uploads the mRNA QC on failed execution run
  */
 process uploadQC_fail {
diff --git a/workflow/conf/multiqc_config.yaml b/workflow/conf/multiqc_config.yaml
index 89059e01682adfcd9354e3c7d78b6a65a87bf569..6dd1cbc262376ab803330a37e6ba36e37ba7e2a7 100644
--- a/workflow/conf/multiqc_config.yaml
+++ b/workflow/conf/multiqc_config.yaml
@@ -103,7 +103,7 @@ custom_data:
     meta:
         file_format: 'tsv'
         section_name: 'Metadata'
-        description: 'This is the comparison of infered metadata, submitter provided, and calculated'
+        description: 'This is the comparison of inferred metadata, submitter provided, and calculated'
         plot_type: 'table'
         pconfig:
             id: 'meta'
diff --git a/workflow/scripts/calculateTPM.R b/workflow/scripts/calculateTPM.R
index a26bf943dce7d082ed03b77939390abb022bba82..0127baa1f0a9e81f355ee8112020411d014ecde5 100644
--- a/workflow/scripts/calculateTPM.R
+++ b/workflow/scripts/calculateTPM.R
@@ -1,3 +1,11 @@
+#!/usr/bin/env R
+#calculateTPM.R
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
+
 gc()
 library(optparse)
 
diff --git a/workflow/scripts/convertGeneSymbols.R b/workflow/scripts/convertGeneSymbols.R
index 6cc5c0a1089881ae1dfd32e248a1ffbcbcd7b24a..17551d35ae74cd32d02ac33f8a491fdf1270af22 100644
--- a/workflow/scripts/convertGeneSymbols.R
+++ b/workflow/scripts/convertGeneSymbols.R
@@ -1,3 +1,11 @@
+#!/usr/bin/env R
+#convertGeneSymbols.R
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
+
 gc()
 library(optparse)
 
diff --git a/workflow/scripts/delete_entry.py b/workflow/scripts/delete_entry.py
index 1b26509a8c1541f65a39e660ec7e6ec158194ef1..77207e810e518ceca3888be8f14793f9891317db 100644
--- a/workflow/scripts/delete_entry.py
+++ b/workflow/scripts/delete_entry.py
@@ -1,3 +1,11 @@
+#!/usr/bin/env python3
+#delete_entry.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
+
 import argparse
 from deriva.core import ErmrestCatalog, get_credential, BaseCLI
 import sys
@@ -34,4 +42,4 @@ if __name__ == '__main__':
     cli.remove_options(["--config-file"])
     host = args.host
     credentials = {"cookie": args.cookie}
-    main(host, 2, credentials)
\ No newline at end of file
+    main(host, 2, credentials)
diff --git a/workflow/scripts/extract_ref_data.py b/workflow/scripts/extract_ref_data.py
index bf06c95696354e6fe5d445718fbfb0769df4182d..87fc1e06ba0e50cac61ade8232d3330998ac9d42 100644
--- a/workflow/scripts/extract_ref_data.py
+++ b/workflow/scripts/extract_ref_data.py
@@ -1,4 +1,10 @@
 #!/usr/bin/env python3
+#extract_ref_data.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import argparse
 import pandas as pd
diff --git a/workflow/scripts/generate_references.py b/workflow/scripts/generate_references.py
index 8e809f1e4471d3393ec4960778d2a210d54c11d1..d72b3522aa1963475b103d32a4087052402edca8 100644
--- a/workflow/scripts/generate_references.py
+++ b/workflow/scripts/generate_references.py
@@ -2,7 +2,7 @@
 #generate_references.py
 #*
 #* --------------------------------------------------------------------------
-#* Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/blob/develop/LICENSE)
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
 #* --------------------------------------------------------------------------
 #*
 
diff --git a/workflow/scripts/generate_versions.py b/workflow/scripts/generate_versions.py
index 2ff498659cc9acbf989ec45e61e8b755b9cc3a66..1ee16837731d88654be0f099a6a4aca9e3264c09 100644
--- a/workflow/scripts/generate_versions.py
+++ b/workflow/scripts/generate_versions.py
@@ -1,11 +1,10 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-#
-# * --------------------------------------------------------------------------
-# * Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/master/LICENSE)
-# * --------------------------------------------------------------------------
-#
+#generate_versions.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 '''Make YAML of software versions.'''
 
diff --git a/workflow/scripts/parse_meta.py b/workflow/scripts/parse_meta.py
index 52f0f18200525f776fe73fcf2f4cd5be8db35045..64f9e559d6768127889055d59b23cc303fcb4e92 100644
--- a/workflow/scripts/parse_meta.py
+++ b/workflow/scripts/parse_meta.py
@@ -1,4 +1,10 @@
 #!/usr/bin/env python3
+#parse_meta.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import argparse
 import pandas as pd
diff --git a/workflow/scripts/tin_hist.py b/workflow/scripts/tin_hist.py
index ee36bb6447dfe0adcdaab60e1224cca5b5a6e246..599f285120911770332034e5ace1dd211c51ecd4 100644
--- a/workflow/scripts/tin_hist.py
+++ b/workflow/scripts/tin_hist.py
@@ -1,4 +1,10 @@
 #!/usr/bin/env python3
+#tin_hist.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import argparse
 import pandas as pd
diff --git a/workflow/scripts/upload_execution_run.py b/workflow/scripts/upload_execution_run.py
index 405c81aa9c2aa31c500157bee3db39413789a7fa..ec5270dc0ef47d73d044953c500769e9d5f401f2 100644
--- a/workflow/scripts/upload_execution_run.py
+++ b/workflow/scripts/upload_execution_run.py
@@ -1,3 +1,11 @@
+#!/usr/bin/env python3
+#upload_execution_run.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
+
 import argparse
 from deriva.core import ErmrestCatalog, get_credential, BaseCLI
 import sys
@@ -33,7 +41,7 @@ def main(hostname, catalog_number, credential):
             "Execution_Status": args.status,
             "Execution_Status_Detail": args.statusDetail.replace('\\n','\n')
         }
-        entities = run_table.insert([run_data])
+        entities = run_table.insert([run_data], add_system_defaults=False, defaults={"RID", "RCT", "RMT"})
         rid = entities[0]["RID"]
     else:
         run_data = {
@@ -58,4 +66,4 @@ if __name__ == '__main__':
     cli.remove_options(["--config-file"])
     host = args.host
     credentials = {"cookie": args.cookie}
-    main(host, 2, credentials)
\ No newline at end of file
+    main(host, 2, credentials)
diff --git a/workflow/scripts/upload_input_bag.py b/workflow/scripts/upload_input_bag.py
index ab4d338074ffec3098667dcf2817041e01ded8bd..ee10cbff8595f8ec5cbe975c133d70a71f4c4897 100644
--- a/workflow/scripts/upload_input_bag.py
+++ b/workflow/scripts/upload_input_bag.py
@@ -1,3 +1,11 @@
+#!/usr/bin/env python3
+#upload_input_bag.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
+
 import argparse
 from deriva.core import ErmrestCatalog, get_credential, BaseCLI
 import sys
@@ -31,7 +39,7 @@ def main(hostname, catalog_number, credential):
         "Bag_Type": "Replicate_Input_Seq"
         }
 
-    entities = inputBag_table.insert([inputBag_data])
+    entities = inputBag_table.insert([inputBag_data], add_system_defaults=False, defaults={"RID", "RCT", "RMT"})
     rid = entities[0]["RID"]
 
     print(rid)
@@ -43,4 +51,4 @@ if __name__ == '__main__':
     cli.remove_options(["--config-file"])
     host = args.host
     credential = {"cookie": args.cookie}
-    main(host, 2, credential)
\ No newline at end of file
+    main(host, 2, credential)
diff --git a/workflow/scripts/upload_output_bag.py b/workflow/scripts/upload_output_bag.py
index e1e1fc1a7fc59e2b003f3c6602f06182c9a3b054..7bd785d3d9ef188b3f4ad05fbf7a03764eb868df 100644
--- a/workflow/scripts/upload_output_bag.py
+++ b/workflow/scripts/upload_output_bag.py
@@ -1,3 +1,11 @@
+#!/usr/bin/env python3
+#upload_output_bag.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
+
 import argparse
 from deriva.core import ErmrestCatalog, get_credential, BaseCLI
 import sys
@@ -34,7 +42,7 @@ def main(hostname, catalog_number, credential):
             "Notes": args.notes,
             "Bag_Type": "mRNA_Replicate_Analysis"
         }
-        entities = outputBag_table.insert([outputBag_data])
+        entities = outputBag_table.insert([outputBag_data], add_system_defaults=False, defaults={"RID", "RCT", "RMT"})
         rid = entities[0]["RID"]
 
     else:
@@ -42,7 +50,7 @@ def main(hostname, catalog_number, credential):
             "RID": args.update,
             "Execution_Run": args.executionRunRID
         }
-        entities = outputBag_table.insert([outputBag_data])
+        entities = outputBag_table.insert([outputBag_data], add_system_defaults=False, defaults={"RID", "RCT", "RMT"})
         rid = entities[0]["RID"]
 
     print(rid)
@@ -54,4 +62,4 @@ if __name__ == '__main__':
     cli.remove_options(["--config-file"])
     host = args.host
     credential = {"cookie": args.cookie}
-    main(host, 2, credential)
\ No newline at end of file
+    main(host, 2, credential)
diff --git a/workflow/scripts/upload_qc.py b/workflow/scripts/upload_qc.py
index 29fac063d9812ad05877d3e8f8f0d865d52eca14..e48d770ea28ebf333b5721676a097b83eabeb492 100644
--- a/workflow/scripts/upload_qc.py
+++ b/workflow/scripts/upload_qc.py
@@ -1,3 +1,11 @@
+#!/usr/bin/env python3
+#upload_qc.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
+
 import argparse
 from deriva.core import ErmrestCatalog, get_credential, BaseCLI
 import sys
@@ -37,14 +45,14 @@ def main(hostname, catalog_number, credential):
             "Median_TIN": args.tin,
             "Notes": args.notes
         }
-        entities = run_table.insert([run_data])
+        entities = run_table.insert([run_data], add_system_defaults=False, defaults={"RID", "RCT", "RMT"})
         rid = entities[0]["RID"]
     elif args.update == "E":
         run_data = {
             "Execution_Run": args.executionRunRID,
             "Replicate": args.repRID
         }
-        entities = run_table.insert([run_data])
+        entities = run_table.insert([run_data], add_system_defaults=False, defaults={"RID", "RCT", "RMT"})
         rid = entities[0]["RID"]
     else:
         run_data = {
@@ -72,4 +80,4 @@ if __name__ == '__main__':
     cli.remove_options(["--config-file"])
     host = args.host
     credentials = {"cookie": args.cookie}
-    main(host, 2, credentials)
\ No newline at end of file
+    main(host, 2, credentials)
diff --git a/workflow/scripts/utils.py b/workflow/scripts/utils.py
index 548b84c0642ee1479c1ac2e968ba1cd1aa9ed660..dc49b345661edf88964a3c3eb491e3f9e17feed9 100644
--- a/workflow/scripts/utils.py
+++ b/workflow/scripts/utils.py
@@ -1,4 +1,10 @@
 #!/usr/bin/env python3
+#utils.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import shlex
 import logging
diff --git a/workflow/tests/test_alignReads.py b/workflow/tests/test_alignReads.py
index 06429a5b8c11daa539499fe1460ef34085031793..4e0b81c0814d2f14ab0ea612b66de544ae2dcec3 100644
--- a/workflow/tests/test_alignReads.py
+++ b/workflow/tests/test_alignReads.py
@@ -1,4 +1,10 @@
 #!/usr/bin/env python3
+#test_alignReads.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd
diff --git a/workflow/tests/test_completion.py b/workflow/tests/test_completion.py
index 25a9941de634d36b84ad750c5968fa75009dfd27..fefa9b9a435f705a81729eb4ff18178461dd430b 100644
--- a/workflow/tests/test_completion.py
+++ b/workflow/tests/test_completion.py
@@ -1,4 +1,10 @@
 #!/usr/bin/env python3
+#test_completion.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd
@@ -12,4 +18,4 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 @pytest.mark.completionMultiqc
 def test_multiqcExist(filename):
     assert os.path.exists(os.path.join(
-        test_output_path, filename))
\ No newline at end of file
+        test_output_path, filename))
diff --git a/workflow/tests/test_consistency.py b/workflow/tests/test_consistency.py
index aa04f19bd23e3749532b87b598179b8f98b2218b..568589f68b857aa9c71606a74601e0ec5690a863 100644
--- a/workflow/tests/test_consistency.py
+++ b/workflow/tests/test_consistency.py
@@ -1,4 +1,10 @@
 #!/usr/bin/env python3
+#test_consistency.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd
diff --git a/workflow/tests/test_dataQC.py b/workflow/tests/test_dataQC.py
index 55df66deaeda6dac18ea26455dd1e3948ceb28ba..ec4409a4333b78cb9d68f1f1cf0be7bcb36a14b7 100644
--- a/workflow/tests/test_dataQC.py
+++ b/workflow/tests/test_dataQC.py
@@ -1,4 +1,10 @@
 #!/usr/bin/env python3
+#test_dataQC.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd
diff --git a/workflow/tests/test_dedupReads.py b/workflow/tests/test_dedupReads.py
index 15e227d4586334721257bc6382d60cf0709bac62..ca299cdcc2bd1c335b26dfaca796047dc80e3e2e 100644
--- a/workflow/tests/test_dedupReads.py
+++ b/workflow/tests/test_dedupReads.py
@@ -1,4 +1,10 @@
 #!/usr/bin/env python3
+#test_dedupReads.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd
diff --git a/workflow/tests/test_downsampleData.py b/workflow/tests/test_downsampleData.py
index 6d98ad656b0bcb0a3e8aee5507149cdcf3cec5f0..1fc9f17a0c9f5084f7d7b35b98ecdb1b8b76e46a 100644
--- a/workflow/tests/test_downsampleData.py
+++ b/workflow/tests/test_downsampleData.py
@@ -1,4 +1,10 @@
 #!/usr/bin/env python3
+#test_downsampleData.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd
diff --git a/workflow/tests/test_fastqc.py b/workflow/tests/test_fastqc.py
index 07e76108fbfc92f945060d8e5d1e1ea8f74e6a4a..86ae3ce5cd56aacb38b62bf547125e6f61fb20ba 100644
--- a/workflow/tests/test_fastqc.py
+++ b/workflow/tests/test_fastqc.py
@@ -1,4 +1,10 @@
 #!/usr/bin/env python3
+#test_fastqc.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd
diff --git a/workflow/tests/test_getBag.py b/workflow/tests/test_getBag.py
index 23bfc0ea50c260a2f5c4cbf62321c066b5743ac2..76f4c6ab1285bfad5ff8da590bbd8bc3c49b8566 100644
--- a/workflow/tests/test_getBag.py
+++ b/workflow/tests/test_getBag.py
@@ -1,4 +1,10 @@
 #!/usr/bin/env python3
+#test_getBag.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd
diff --git a/workflow/tests/test_getData.py b/workflow/tests/test_getData.py
index 596a120abe904eac8f3e0ad871c9f8c03a6cba5f..f89d9c97003aa278476ea536fa49c02d440bb2b5 100644
--- a/workflow/tests/test_getData.py
+++ b/workflow/tests/test_getData.py
@@ -1,4 +1,10 @@
 #!/usr/bin/env python3
+#test_getData.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd
diff --git a/workflow/tests/test_inferMetadata.py b/workflow/tests/test_inferMetadata.py
index 7485163631e2604ac2d5477a5c27b2fc9b235b44..e10be1734129e592a9f7d6b23254ac0535106330 100644
--- a/workflow/tests/test_inferMetadata.py
+++ b/workflow/tests/test_inferMetadata.py
@@ -1,4 +1,10 @@
 #!/usr/bin/env python3
+#test_inferMetadata.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd
diff --git a/workflow/tests/test_makeBigWig.py b/workflow/tests/test_makeBigWig.py
index 273b2cdbb892a464a26b152db2c5d5c0a46922bf..2b72fc53604b7b28b9239235f4b20b32d0ed0421 100644
--- a/workflow/tests/test_makeBigWig.py
+++ b/workflow/tests/test_makeBigWig.py
@@ -1,4 +1,10 @@
 #!/usr/bin/env python3
+#test_makeBigWig.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd
diff --git a/workflow/tests/test_makeFeatureCounts.py b/workflow/tests/test_makeFeatureCounts.py
index 43e6810482d6131b064b3604c95e89e9296db603..2aa54b9d3742e18b074b84d7314f6938460f41c3 100644
--- a/workflow/tests/test_makeFeatureCounts.py
+++ b/workflow/tests/test_makeFeatureCounts.py
@@ -1,4 +1,10 @@
 #!/usr/bin/env python3
+#test_makeFeatureCounts.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd
diff --git a/workflow/tests/test_outputBag.py b/workflow/tests/test_outputBag.py
index c73e6474efdb9093b0cc66c00b220426be707690..a633294aef9bbe96c48b734571775eee7e48bf37 100644
--- a/workflow/tests/test_outputBag.py
+++ b/workflow/tests/test_outputBag.py
@@ -1,4 +1,10 @@
 #!/usr/bin/env python3
+#test_outputBag.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd
diff --git a/workflow/tests/test_parseMetadata.py b/workflow/tests/test_parseMetadata.py
index 738f5ec66ee4e08d4e64400da719b759a7876a37..1db3a3141683c28820e33731150ba6eb83a7f999 100644
--- a/workflow/tests/test_parseMetadata.py
+++ b/workflow/tests/test_parseMetadata.py
@@ -1,4 +1,10 @@
 #!/usr/bin/env python3
+#test_parseMetadata.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd
diff --git a/workflow/tests/test_seqwho.py b/workflow/tests/test_seqwho.py
index 051cc4b379bc2378b2effff22f4737592d9b54cd..c35d119a541bd7a5d7777bc77e565bfcc1da59d9 100644
--- a/workflow/tests/test_seqwho.py
+++ b/workflow/tests/test_seqwho.py
@@ -1,4 +1,10 @@
 #!/usr/bin/env python3
+#test_seqwho.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd
diff --git a/workflow/tests/test_trimData.py b/workflow/tests/test_trimData.py
index a0938e756715fb30254e5c72fee4cd38bffec330..fe7072a8039b6efb2291d23ebcb20b6444ecfb30 100644
--- a/workflow/tests/test_trimData.py
+++ b/workflow/tests/test_trimData.py
@@ -1,4 +1,10 @@
 #!/usr/bin/env python3
+#test_trimData.py
+#*
+#* --------------------------------------------------------------------------
+#* Licensed under MIT (https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/14a1c222e53f59391d96a2a2e1fd4995474c0d15/LICENSE)
+#* --------------------------------------------------------------------------
+#*
 
 import pytest
 import pandas as pd