Markdown

.github/markdownlint.yml

@@ -1,12 +1,5 @@
 # Markdownlint configuration file
-default: true
+default: true,
 line-length: false
 no-duplicate-header:
     siblings_only: true
-no-inline-html:
-    allowed_elements:
-        - img
-        - p
-        - kbd
-        - details
-        - summary

.github/workflows/ci.yml

@@ -72,15 +72,33 @@ jobs:
           # Nextflow versions: check pipeline minimum and current latest
           nxf_ver: ['20.10.0', '']
           parameters: 
-            - '--edyeet_map_pct_id 70'
+            - '--alignment_map_pct_id 70'
             - '--edyeet_align_pct_id 70'
-            - '--edyeet_n_secondary 2'
-            - '--edyeet_segment_length 5000'
-            - '--edyeet_merge_segments'
-            - '--edyeet_no_splits'
+            - '--alignment_n_secondary 2'
+            - '--alignment_segment_length 5000'
+            - '--alignment_merge_segments'
+            - '--alignment_no_splits'
+            - '--alingment_block_length 40000'
       steps:
         - name: Check out pipeline code
           uses: actions/checkout@v2
+
+        - name: Check if Dockerfile or Conda environment changed
+          uses: technote-space/get-diff-action@v4
+          with:
+            FILES: |
+              Dockerfile
+              environment.yml
+
+        - name: Build new docker image
+          if: env.MATCHED_FILES
+          run: docker build --no-cache . -t nfcore/pangenome:dev
+
+        - name: Pull docker image
+          if: ${{ !env.MATCHED_FILES }}
+          run: |
+            docker pull nfcore/pangenome:dev
+            docker tag nfcore/pangenome:dev nfcore/pangenome:dev
 
         - name: Install Nextflow
           run: |
@@ -89,6 +107,52 @@ jobs:
         - name: Run pipeline with edyeet and various parameters
           run: |
             nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }}
+  wfmash:
+      name: Test wfmash with workflow parameters
+      if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/pangenome') }}
+      runs-on: ubuntu-latest
+      env:
+        NXF_VER: ${{ matrix.nxf_ver }}
+        NXF_ANSI_LOG: false
+      strategy:
+        matrix:
+          # Nextflow versions: check pipeline minimum and current latest
+          nxf_ver: ['20.10.0', '']
+          parameters: 
+            - '--wfmash --alignment_map_pct_id 70'
+            - '--wfmash --alignment_n_secondary 2'
+            - '--wfmash --alignment_segment_length 5000'
+            - '--wfmash --alignment_merge_segments'
+            - '--wfmash --alignment_no_splits'
+            - '--wfmash --alingment_block_length 40000'
+      steps:
+        - name: Check out pipeline code
+          uses: actions/checkout@v2
+
+        - name: Check if Dockerfile or Conda environment changed
+          uses: technote-space/get-diff-action@v4
+          with:
+            FILES: |
+              Dockerfile
+              environment.yml
+
+        - name: Build new docker image
+          if: env.MATCHED_FILES
+          run: docker build --no-cache . -t nfcore/pangenome:dev
+
+        - name: Pull docker image
+          if: ${{ !env.MATCHED_FILES }}
+          run: |
+            docker pull nfcore/pangenome:dev
+            docker tag nfcore/pangenome:dev nfcore/pangenome:dev
+
+        - name: Install Nextflow
+          run: |
+            wget -qO- get.nextflow.io | bash
+            sudo mv nextflow /usr/local/bin/
+        - name: Run pipeline with wfmash and various parameters
+          run: |
+            nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }}            
   seqwish:
       name: Test seqwish with workflow parameters
       if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/pangenome') }}
@@ -102,11 +166,28 @@ jobs:
           nxf_ver: ['20.10.0', '']
           parameters: 
             - '--seqwish_min_match_length 13'
-            - '--seqwish_transclose_batch 1000'
+            - '--seqwish_transclose_batch 10000'
       steps:
         - name: Check out pipeline code
           uses: actions/checkout@v2
 
+        - name: Check if Dockerfile or Conda environment changed
+          uses: technote-space/get-diff-action@v4
+          with:
+            FILES: |
+              Dockerfile
+              environment.yml
+
+        - name: Build new docker image
+          if: env.MATCHED_FILES
+          run: docker build --no-cache . -t nfcore/pangenome:dev
+
+        - name: Pull docker image
+          if: ${{ !env.MATCHED_FILES }}
+          run: |
+            docker pull nfcore/pangenome:dev
+            docker tag nfcore/pangenome:dev nfcore/pangenome:dev
+
         - name: Install Nextflow
           run: |
             wget -qO- get.nextflow.io | bash
@@ -128,15 +209,33 @@ jobs:
           parameters: 
             - '--smoothxg_max_block_weight 20000'
             - '--smoothxg_max_path_jump 10000'
-            - '--smoothxg_min_subpath 0'
             - '--smoothxg_max_edge_jump 6000'
-            - '--smoothxg_max_poa_length 11111'
-            - '--smoothxg_consensus_jump_max 11,111,1111,11111'
+            - '--smoothxg_max_poa_length 20000'
+            - '--smoothxg_consensus_spec 11,111,1111,11111'
             - '--smoothxg_block_id_min 0.7'
+            - '--smoothxg_ratio_contain 0.3'
+            - '--smoothxg_poa_params 2,4,6,2,24,1'
       steps:
         - name: Check out pipeline code
           uses: actions/checkout@v2
 
+        - name: Check if Dockerfile or Conda environment changed
+          uses: technote-space/get-diff-action@v4
+          with:
+            FILES: |
+              Dockerfile
+              environment.yml
+
+        - name: Build new docker image
+          if: env.MATCHED_FILES
+          run: docker build --no-cache . -t nfcore/pangenome:dev
+
+        - name: Pull docker image
+          if: ${{ !env.MATCHED_FILES }}
+          run: |
+            docker pull nfcore/pangenome:dev
+            docker tag nfcore/pangenome:dev nfcore/pangenome:dev
+
         - name: Install Nextflow
           run: |
             wget -qO- get.nextflow.io | bash

Dockerfile

@@ -1,4 +1,4 @@
-FROM ghcr.io/pangenome/pggb:202012122000576ef861
+FROM ghcr.io/pangenome/pggb:20210225173013c37223
 LABEL authors="Simon Heumos, Michael Heuer, Lukas Heumos, Erik Garrison, Andrea Guarracino" \
       description="Docker image containing all software requirements for the nf-core/pangenome pipeline"
 

README.md

@@ -43,7 +43,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 5. Start running your own analysis!
 
     ```bash
-    nextflow run nf-core/pangenome -profile <docker/singularity/podman/conda/institute> --input '*.fa.gz'
+    nextflow run nf-core/pangenome -profile <docker/singularity/podman/conda/institute> --input 'input.fa.gz'
     ```
 
 See [usage docs](https://nf-co.re/pangenome/usage) for all of the available options when running the pipeline.