Merge nf-test into main

.github/workflows/ci-tests.yml

@@ -0,0 +1,35 @@
+name: CI Tests
+
+on: [push, pull_request]
+
+jobs:
+
+  test:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        shard: [1, 2, 3, 4, 5]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Set up JDK 11
+        uses: actions/setup-java@v2
+        with:
+          java-version: '11'
+          distribution: 'adopt'
+
+      - name: Setup Nextflow
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "latest-edge"
+
+      - name: Install nf-test
+        run: |
+          wget -qO- get.nf-test.com | bash  -s 0.9.0-rc2
+          sudo mv nf-test /usr/local/bin/
+
+      - name: Run Tests (Shard ${{ matrix.shard }}/${{ strategy.job-total }})
+        run: nf-test test --ci --shard ${{ matrix.shard }}/${{ strategy.job-total }}

.gitignore

@@ -0,0 +1,7 @@
+work
+.nextflow
+.nextflow.*
+tests/output
+.nf-test/
+nf-test
+.nf-test.log

config/base.config

@@ -4,7 +4,7 @@
 // PROCESS RESOURCES
 process {
 	withName: "POLISH_CLUSTER" {
-		memory = { 1.GB * task.attempt }
+		memory = { 2.GB * task.attempt }
 		cpus = 1
 	}
 

config/test.config

@@ -12,14 +12,15 @@ params {
 	version 		= false
 	debug 			= false
 
-	input 			= "$baseDir/data/fastq_pass/"
-	output 			= "umi-pipeline-nf_test-run"
-	reference 		= "$baseDir/data/ref/lpa-ref2645.fasta"
-	reference_fai 		= "$baseDir/data/ref/lpa-ref2645.fasta.fai"
-	bed 			= "$baseDir/data/ref/lpa-ref2645.bed"
+	input 			= "$baseDir/tests/input/pipeline/fastq_pass/"
+	output 			= "test_umi-pipeline-nf"
+	reference 		= "$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta"
+	reference_fai 	= "$baseDir/tests/input/pipeline/ref/lpa-ref2645.fasta.fai"
+	bed 			= "$baseDir/tests/input/pipeline/ref/lpa-ref2645.bed"
 
 	min_reads_per_cluster 	= 10
 	max_reads_per_cluster 	= 20
+	min_reads_per_barcode = 0
 	call_variants 		= true
 	variant_caller 		= "freebayes"
 }

env/Dockerfile

@@ -19,5 +19,3 @@ RUN conda update -y conda && \
 
 WORKDIR "/opt"
 RUN wget https://github.com/seppinho/mutserve/releases/download/v2.0.0-rc13.lpa/mutserve_LPA_adapted.jar
-
-

lib/processes/cluster.nf

@@ -3,16 +3,17 @@ vsearch_dir="vsearch_clusters"
 
 process CLUSTER {
     publishDir "${params.output}/${sample}/clustering/${type}", pattern: "${consensus_fasta}", mode: 'copy'
+    publishDir "${params.output}/${sample}/clustering/${type}", pattern: "cluster*", mode: 'copy'
 
     input:
         tuple val( sample ), val( target ), path( detected_umis_fastq )
         val ( type )
     output:
-        tuple val( "${sample}" ), val( "${target}" ), path( "${consensus_fasta}" ), emit:consensus_fasta
-        tuple val( "${sample}" ), val( "${target}" ), path( "cluster*" ), emit:cluster_fastas
+        tuple val( "${sample}" ), val( "${target}" ), path( "${consensus_fasta}" ), optional: true, emit:consensus_fasta
+        tuple val( "${sample}" ), val( "${target}" ), path( "cluster*" ), optional: true, emit:cluster_fastas
 
     script:
-        def id = "${type}" == "raw" ? 0.8 : 0.99
+        def id = "${type}" == "raw" ? 0.90 : 0.99
     """
         vsearch \
         --clusterout_id \

lib/processes/variant_calling/lofreq.nf → lib/processes/lofreq.nf

@@ -16,6 +16,8 @@ process LOFREQ {
       --ref ${reference} \
       --out ${type}.vcf \
       --call-indels \
+      --min-cov 5 \
+      --no-default-filter \
       ${bam}
     """
 }

lib/processes/reformat_filter_cluster.nf

@@ -1,6 +1,6 @@
 process REFORMAT_FILTER_CLUSTER {
     tag "${sample}"
-    // publishDir "${params.output}/${sample}/clustering/${type}/smolecule", pattern: "smolecule*", mode: 'copy'
+    publishDir "${params.output}/${sample}/clustering/${type}/smolecule", pattern: "smolecule*", mode: 'copy'
     publishDir "${params.output}/${sample}/stats/${type}", pattern: "*tsv", mode: 'copy'
 
     input:

lib/workflows/umi-pipeline.nf

@@ -51,9 +51,9 @@ include {REFORMAT_FILTER_CLUSTER} from '../processes/reformat_filter_cluster.nf'
 include {POLISH_CLUSTER} from '../processes/polish_cluster.nf'
 include {FILTER_CONSENSUS_FASTQ} from '../processes/filter_consensus_fastq.nf'
 include {REFORMAT_CONSENSUS_CLUSTER} from '../processes/reformat_consensus_cluster.nf'
-include {LOFREQ as LOFREQ_CONSENSUS; LOFREQ as LOFREQ_FINAL_CONSENSUS} from '../processes/variant_calling/lofreq.nf'
-include {MUTSERVE as MUTSERVE_CONSENSUS; MUTSERVE as MUTSERVE_FINAL_CONSENSUS} from '../processes/variant_calling/mutserve.nf'
-include {FREEBAYES as FREEBAYES_CONSENSUS; FREEBAYES as FREEBAYES_FINAL_CONSENSUS} from '../processes/variant_calling/freebayes.nf'
+include {LOFREQ as LOFREQ_CONSENSUS; LOFREQ as LOFREQ_FINAL_CONSENSUS} from '../processes/lofreq.nf'
+include {MUTSERVE as MUTSERVE_CONSENSUS; MUTSERVE as MUTSERVE_FINAL_CONSENSUS} from '../processes/mutserve.nf'
+include {FREEBAYES as FREEBAYES_CONSENSUS; FREEBAYES as FREEBAYES_FINAL_CONSENSUS} from '../processes/freebayes.nf'
 
 
 // SUB-WORKFLOWS

nextflow.config

@@ -54,7 +54,7 @@ params {
     medaka_model                          = "r1041_e82_400bps_hac_g615"
     fwd_umi                               = "TTTVVVVTTVVVVTTVVVVTTVVVVTTT"
     rev_umi                               = "AAABBBBAABBBBAABBBBAABBBBAAA"
-    adapter_length                        = 200
+    adapter_length                        = 100
     min_length                            = 40
     max_length                            = 60
     minimap2_param                        = "-ax map-ont -k 13 --MD"
@@ -65,37 +65,32 @@ params {
 // NEXTFLOW PROFILES
 
 // Load base.config by default for all pipelines
-includeConfig "${baseDir}/config/base.config"
+includeConfig "config/base.config"
 
 process.container                         = 'quay.io/genepi/umi-pipeline-nf:v0.2.1'
 
 profiles {
 
-    // -profile conda
     conda {
-        process.conda                        = "${baseDir}/env/environment.yml"
+        process.conda                        = "env/environment.yml"
     }
 
-    // -profile docker
     docker {
         docker.enabled                       = true
     }
 
-    // -profile singularity
     singularity {
         singularity.enabled                   = true
         singularity.autoMounts                = true
         docker.enabled                        = false
     }
 
-    // -profile test
     test {
-        includeConfig "${baseDir}/config/test.config"
+        includeConfig "config/test.config"
     }
 
-    // -profile custom
     custom {
-        includeConfig "${baseDir}/config/custom.config"
+        includeConfig "config/custom.config"
     }
 
 }

nf-test.config

@@ -0,0 +1,8 @@
+config {
+
+    testsDir "tests"
+    workDir ".nf-test"
+    configFile "tests/nextflow.config"
+    profile "test,docker"
+
+}