update workflow

cidgoh · Dec 16, 2024 · 770e250 · 770e250
1 parent bdc1cd9
commit 770e250
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Showing 11 changed files with 11 additions and 44 deletions.
diff --git a/.github/workflows/nextflow_CI.yml b/.github/workflows/nextflow_CI.yml
@@ -17,25 +17,9 @@ jobs:
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
 
-      - name: Install Singularity
-        run: |
-          sudo apt-get update && sudo apt-get install -y \
-            build-essential \
-            libssl-dev \
-            uuid-dev \
-            libgpgme11-dev \
-            squashfs-tools \
-            libseccomp-dev \
-            wget \
-            pkg-config \
-            git \
-            cryptsetup
-          wget https://github.com/sylabs/singularity/releases/download/v3.10.0/singularity-ce_3.10.0-focal_amd64.deb
-          sudo dpkg -i singularity-ce_3.10.0-focal_amd64.deb
-
       - name: Run pipeline test (user)
         run: |
-          nextflow run main.nf -profile singularity --prefix "covidmvp-user-$(date +%Y-%m-%d)" -params-file covidmvp_user.yaml
+          nextflow run main.nf -profile docker --prefix "covidmvp-user-$(date +%Y-%m-%d)" -params-file covidmvp_user.yaml
 
   test_sarscov2_reference:
     name: Run pipeline test (reference)
@@ -48,22 +32,6 @@ jobs:
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
 
-      - name: Install Singularity
-        run: |
-          sudo apt-get update && sudo apt-get install -y \
-            build-essential \
-            libssl-dev \
-            uuid-dev \
-            libgpgme11-dev \
-            squashfs-tools \
-            libseccomp-dev \
-            wget \
-            pkg-config \
-            git \
-            cryptsetup
-          wget https://github.com/sylabs/singularity/releases/download/v3.10.0/singularity-ce_3.10.0-focal_amd64.deb
-          sudo dpkg -i singularity-ce_3.10.0-focal_amd64.deb
-
       - name: Run pipeline test (reference)
         run: |
-          nextflow run main.nf -profile singularity --prefix "covidmvp-$(date +%Y-%m-%d)" -params-file covidmvp_clinical_params.yaml
+          nextflow run main.nf -profile docker --prefix "covidmvp-$(date +%Y-%m-%d)" --end_date $(date +%Y-%m-%d) -params-file covidmvp_clinical_params.yaml
diff --git a/conf/profiles.config b/conf/profiles.config
@@ -65,7 +65,7 @@ profiles {
     }
     wave {
         wave.enabled           = true
-        wave.strategy          = ['singularity', 'container']
+        wave.strategy          = ['singularity']
     }
     eagle     { includeConfig 'eagle.config'     }
 }
diff --git a/covidmvp_clinical_params.yaml b/covidmvp_clinical_params.yaml
@@ -8,7 +8,6 @@ skip_postprocessing: false
 skip_posting: true
 skip_harmonize: true
 start_date: "2020-01-01"
-end_date: "(date +%Y-%m-%d)"
 metadata_source: "ViralAi_EpiCoV"
 metadata_config: "metadata_conf/metadata.yaml"
 outdir: "results/covidmvp"

diff --git a/modules/local/convertgff2json.nf b/modules/local/convertgff2json.nf
@@ -8,7 +8,7 @@ process CONVERTGFFTOJSON {
     conda "conda-forge::pandas=1.4.3"
     container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
         ? 'https://depot.galaxyproject.org/singularity/pandas:1.4.3'
-        : 'community.wave.seqera.io/library/pip_pandas:f80b46869e03f6ef'}"
+        : 'amancevice/pandas:1.4.3'}"
 
     input:
     tuple val(meta), path(gff)

diff --git a/modules/local/extractMetadata.nf b/modules/local/extractMetadata.nf
@@ -3,7 +3,7 @@ process EXTRACTMETADATA {
     conda "conda-forge::pandas=1.4.3"
     container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
         ? 'https://depot.galaxyproject.org/singularity/pandas:1.4.3'
-        : 'community.wave.seqera.io/library/pip_pandas:f80b46869e03f6ef'}"
+        : 'amancevice/pandas:1.4.3'}"
 
     input:
     tuple val(meta), path(metadata)

diff --git a/modules/local/extractVariants.nf b/modules/local/extractVariants.nf
@@ -3,7 +3,7 @@ process EXTRACTVARIANTS {
       conda "conda-forge::pandas=1.4.3"
       container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
             ? 'https://depot.galaxyproject.org/singularity/pandas:1.4.3'
-            : 'community.wave.seqera.io/library/pip_pandas:f80b46869e03f6ef'}"
+            : 'amancevice/pandas:1.4.3'}"
 
       input:
       tuple val(meta), path(variants)

diff --git a/modules/local/harmonize_metadata.nf b/modules/local/harmonize_metadata.nf
@@ -4,7 +4,7 @@ process METADATA_HARMONIZER {
     conda "conda-forge::pandas=1.4.3"
     container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
         ? 'https://depot.galaxyproject.org/singularity/pandas:1.4.3'
-        : 'community.wave.seqera.io/library/pip_pandas:f80b46869e03f6ef'}"
+        : 'amancevice/pandas:1.4.3'}"
 
     input:
     tuple val(meta), path(metadata)

diff --git a/modules/local/merge_classification_report.nf b/modules/local/merge_classification_report.nf
@@ -3,7 +3,7 @@ process MERGE_CLASSIFFICATION_METADATA {
     conda "conda-forge::pandas=1.4.3"
     container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
         ? 'https://depot.galaxyproject.org/singularity/pandas:1.4.3'
-        : 'community.wave.seqera.io/library/pip_pandas:f80b46869e03f6ef'}"
+        : 'amancevice/pandas:1.4.3'}"
 
     input:
     tuple val(meta), path(metadata)

diff --git a/modules/local/splitmutations_gvf.nf b/modules/local/splitmutations_gvf.nf
@@ -5,7 +5,7 @@ process NCOVSPLITMUTATIONSGVF {
   conda "conda-forge::pandas=1.4.3"
   container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
     ? 'https://depot.galaxyproject.org/singularity/pandas:1.4.3'
-    : 'community.wave.seqera.io/library/pip_pandas:f80b46869e03f6ef'}"
+    : 'amancevice/pandas:1.4.3'}"
 
   input:
   tuple val(meta), path(gvf)

diff --git a/modules/local/splitmutations_pokay.nf b/modules/local/splitmutations_pokay.nf
@@ -5,7 +5,7 @@ process NCOVSPLITMUTATIONSPOKAY {
   conda "conda-forge::pandas=1.4.3"
   container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
     ? 'https://depot.galaxyproject.org/singularity/pandas:1.4.3'
-    : 'community.wave.seqera.io/library/pip_pandas:f80b46869e03f6ef'}"
+    : 'amancevice/pandas:1.4.3'}"
 
   input:
   tuple val(meta), path(annotations)

diff --git a/modules/local/vcftogvf.nf b/modules/local/vcftogvf.nf
@@ -3,7 +3,7 @@ process VCFTOGVF {
   conda "conda-forge::pandas=1.4.3"
   container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
     ? 'https://depot.galaxyproject.org/singularity/pandas:1.4.3'
-    : 'community.wave.seqera.io/library/pip_pandas:f80b46869e03f6ef'}"
+    : 'amancevice/pandas:1.4.3'}"
 
   input:
   tuple val(meta), path(vcf)