initial pass of fixes

.github/workflows/awsfulltest.yml

@@ -24,7 +24,7 @@ jobs:
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnasplice/results-${{ github.sha }}"
             }
-          profiles: test_full,aws_tower
+          profiles: test_full
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file

.github/workflows/awstest.yml

@@ -22,7 +22,7 @@ jobs:
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnasplice/results-test-${{ github.sha }}"
             }
-          profiles: test,aws_tower
+          profiles: test
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file

.github/workflows/ci.yml

@@ -36,8 +36,5 @@ jobs:
           version: "${{ matrix.NXF_VER }}"
 
       - name: Run pipeline with test data
-        # TODO nf-core: You can customise CI pipeline run tests as required
-        # For example: adding multiple test runs with different parameters
-        # Remember that you can parallelise this by using strategy.matrix
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results

CHANGELOG.md

@@ -9,17 +9,6 @@ First release of nf-core/rnasplice, created with the [nf-core](https://nf-co.re/
 
 ### `Added`
 
-- Visualization of differential results with edgeR, DEXSeq, and MISO
-- Contrasts specified using contrastsheet.csv
-- Allow users to specify input data type and start point (e.g., fastq, genome_bam, transcript_bam, salmon_results)
-- Pipeline schematic updated
-
-## v1.0dev - [2022-11-10]
-
-Development release of nf-core/rnasplice, created with the [nf-core](https://nf-co.re/) template.
-
-### `Added`
-
 Implemented pipeline:
 
 - Merge re-sequenced FastQ files (cat)
@@ -45,3 +34,10 @@ Implemented pipeline:
 - Event-based splicing analysis:
   - STAR -> rMATS
   - Salmon -> SUPPA2
+
+Updated pipeline:
+
+- Visualization of differential results with edgeR, DEXSeq, and MISO
+- Contrasts specified using contrastsheet.csv
+- Allow users to specify input data type and start point (e.g., fastq, genome_bam, transcript_bam, salmon_results)
+- Pipeline schematic updated

README.md

@@ -14,7 +14,7 @@
 
 **nf-core/rnasplice** is a bioinformatics pipeline for alternative splicing analysis of RNA sequencing data obtained from organisms with a reference genome and annotation.
 
-![nf-core/rnasplice metro map](assets/rnasplice_map.png)
+![nf-core/rnasplice metro map](docs/rnasplice_map.png)
 
 1. Merge re-sequenced FastQ files ([`cat`](http://www.linfo.org/cat.html))
 2. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))