test new snakemake with report reinstated

ktmeaton · Nov 4, 2020 · e525b80 · e525b80
1 parent db159f7
commit e525b80
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Showing 4 changed files with 38 additions and 30 deletions.
diff --git a/.github/workflows/pipeline.yaml b/.github/workflows/pipeline.yaml
@@ -65,18 +65,18 @@ jobs:
             conda activate plague-phylogeography;
             snakemake --profile profiles/gh-actions all;
       # run report
-      #- name: run report
-      #  shell: bash -l {0}
-      #  run: |
-      #      conda activate plague-phylogeography;
-      #      snakemake --profile profiles/gh-actions --report workflow/report/report.html all;
+      - name: run report
+        shell: bash -l {0}
+        run: |
+            conda activate plague-phylogeography;
+            snakemake --profile profiles/gh-actions --report workflow/report/report.html all;
       #------------------------------------------------------------------------#
       #  Artifact Upload
-      #- name: artifact conda-report
-      #  uses: actions/upload-artifact@v2
-      #  with:
-      #    name: conda-report
-      #    path: workflow/report/report.html
+      - name: artifact conda-report
+        uses: actions/upload-artifact@v2
+        with:
+          name: conda-report
+          path: workflow/report/report.html
   #----------------------------------------------------------------------------#
   pipeline_singularity:
     name: Pipeline with Singularity
@@ -117,16 +117,16 @@ jobs:
       - name: run all
         run: singularity exec plague-phylogeography_dev.sif snakemake --profile profiles/gh-actions all;
       # run report
-      #- name: run report
-      #  shell: bash -l {0}
-      #  run: singularity exec plague-phylogeography_dev.sif snakemake --profile profiles/gh-actions --report workflow/report/report.html all;
+      - name: run report
+        shell: bash -l {0}
+        run: singularity exec plague-phylogeography_dev.sif snakemake --profile profiles/gh-actions --report workflow/report/report.html all;
       #------------------------------------------------------------------------#
       #  Artifact Upload
-      #- name: artifact singularity-report
-      #  uses: actions/upload-artifact@v2
-      #  with:
-      #    name: singularity-report
-      #    path: workflow/report/report.html
+      - name: artifact singularity-report
+        uses: actions/upload-artifact@v2
+        with:
+          name: singularity-report
+          path: workflow/report/report.html
   #----------------------------------------------------------------------------#
   pipeline_docker:
     name: Pipeline with Docker
@@ -157,13 +157,13 @@ jobs:
         shell: bash -l {0}
         run: docker run -v $PWD:/pipeline -w /pipeline ktmeaton/plague-phylogeography:dev snakemake --profile profiles/gh-actions all;
       # run report
-      #- name: run report
-      #  shell: bash -l {0}
-      #  run: docker run -v $PWD:/pipeline -w /pipeline ktmeaton/plague-phylogeography:dev snakemake --profile profiles/gh-actions --report workflow/report/report.html all;
+      - name: run report
+        shell: bash -l {0}
+        run: docker run -v $PWD:/pipeline -w /pipeline ktmeaton/plague-phylogeography:dev snakemake --profile profiles/gh-actions --report workflow/report/report.html all;
       #------------------------------------------------------------------------#
       #  Artifact Upload
-      #- name: artifact docker-report
-      #  uses: actions/upload-artifact@v2
-      #  with:
-      #    name: docker-report
-      #    path: workflow/report/report.html
+      - name: artifact docker-report
+        uses: actions/upload-artifact@v2
+        with:
+          name: docker-report
+          path: workflow/report/report.html
diff --git a/docs-new/main.md b/docs-new/main.md
@@ -78,14 +78,21 @@ snakemake --profile profiles/infoserv multiqc_assembly
 ### Modern Assembly (Local)
 
 Construct alignments of the Institute Pasteur *Y. pestis* samples.
+nf-core/eager parameters need to be modified:
+
+```bash
+remove: --mergedonly
+add: --clip_forward_adaptor CTGTCTCTTATACACATCT
+add: --clip_reverse_adaptor CTGTCTCTTATACACATCT
+```
 
 - [ ] Align to the reference genome and create a final MultiQC report.
 
 ```bash
 snakemake --profile profiles/infoserve multiqc_local
 ```
 
-- [x] Identify low coverage samples (<70% at 10X) by marking the BioSampleComment as "REMOVE: Assembly Modern Low Coverage".
+- [x] Identify low coverage samples (<70% at 10X) by marking the BioSampleComment as "REMOVE: Assembly Local Low Coverage".
 
 - [ ] Create a filtered MultiQC report.
 
@@ -119,7 +126,8 @@ snakemake --profile profiles/infoserv multiqc_sra
 
 SAMN00715800 (8291)
 
-Split the single end fastq into forward and reverse reads.
+Split the single end fastq into forward and reverse reads. Cutadapt is
+not necessary! Could use AdapterRemoval.
 
 ```bash
 mv results/data/sra/SAMN00715800/SRR341961_1.fastq.gz results/data/sra/SAMN00715800/SRR341961_untrimmed.fastq.gz

diff --git a/workflow/envs/main/environment.yaml b/workflow/envs/main/environment.yaml
@@ -8,7 +8,7 @@ dependencies:
   # Snakemake Execution
   - python=3.7.3
   - sqlite=3.31.1
-  - snakemake=5.26.1 # Update to 5.27.3 when available on conda
+  - snakemake=5.27.4
   - flask=1.1.2
   - python-dotenv=0.14.0
   - slackclient=2.9.1

diff --git a/workflow/envs/merge/environment.yaml b/workflow/envs/merge/environment.yaml
@@ -67,7 +67,7 @@ dependencies:
 - samtools=1.10
 - singularity=3.6.3
 - slackclient=2.9.1
-- snakemake=5.26.1 # Update to 5.27.3 when available on conda
+- snakemake=5.27.4
 - sqlite=3.31.1
 - vcftools=0.1.16
 - pip: