Update CHANGELOG.md and ci.yml

peterk87 · Aug 7, 2024 · 968641e · 968641e
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -35,6 +35,12 @@ jobs:
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v4
+      - name: pre - df, Docker df, Docker images
+        if: ${{ always() }}
+        run: |
+          df -h
+          docker system df
+          docker images
       - name: Cache Nextflow binary
         uses: actions/cache@v4
         id: cache-nextflow
@@ -90,6 +96,12 @@ jobs:
             -profile test_illumina,docker \
             --ncbi_influenza_fasta influenza-10k.fna.zst \
             --ncbi_influenza_metadata influenza.csv.zst
+      - name: post - df, Docker df, Docker images
+        if: ${{ always() }}
+        run: |
+          df -h
+          docker system df
+          docker images
       - name: Upload Artifact
         if: success()
         uses: actions/upload-artifact@v4
@@ -117,6 +129,12 @@ jobs:
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v4
+      - name: pre - df, Docker df, Docker images
+        if: ${{ always() }}
+        run: |
+          df -h
+          docker system df
+          docker images
       - name: Cache Nextflow binary
         uses: actions/cache@v4
         id: cache-nextflow
@@ -210,6 +228,12 @@ jobs:
             --ncbi_influenza_metadata influenza.csv.zst
       - name: Tree of results
         run: tree -h results/
+      - name: post - df, Docker df, Docker images
+        if: ${{ always() }}
+        run: |
+          df -h
+          docker system df
+          docker images
       - name: Upload .nextflow.log
         uses: actions/upload-artifact@v4
         with:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -12,6 +12,8 @@ to Q-score lines beginning with `@`.
 
 * fix: updated Perl regex to better match Illumina FASTQ header lines starting with `@`. At least one space ` ` is expected in the header line. Match regex has been changed to `/^@.* .*/` from `/^@.*/` so hopefully Q-score lines should not be matched anymore.
 * dev: replaced nf-core/modules DUMPSOFTWAREVERSIONS with [mqc_versions_table v0.2.0](https://github.com/CFIA-NCFAD/nim-mqc-versions-yml/releases/tag/0.2.0) Nim statically compiled binary to parse `versions.yml` and output necessary YAML with HTML content for display of process and tool versions table in MultiQC report. In theory DUMPSOFTWAREVERSIONS should be using the same Docker/Singularity image/Conda env as the MultiQC process, but DUMPSOFTWAREVERSIONS uses an older version of MultiQC and only uses it for the pyyaml library. `mqc_versions_table` was developed to handle this instead with a small 200KB binary instead.
+* dev: harmonize Docker/Singularity containers and Conda envs used across processes.
+* ci: use `symlink` mode for `publishDir` by default for `test_nanopore.config` and `test_illumina.config` to limit disk usage during CI.
 
 ## [[3.4.0](https://github.com/CFIA-NCFAD/nf-flu/releases/tag/3.4.0)] - 2024-07-24