Merge branch 'main' into edge_v3

main.nf

@@ -9,8 +9,7 @@ include {READSTOCONTIGS} from './modules/runReadsToContig/runReadsToContig.nf'
 
 workflow {
 
-    //input specification
-
+    //input specification    
     fastqFiles = channel.fromPath(params.shared.inputFastq, checkIfExists:true)
     contigs = channel.empty()
     if(params.r2c.useAssembledContigs) {
@@ -33,6 +32,7 @@ workflow {
     unpaired = channel.empty()
     if(params.modules.faqcs) {
         FAQCS(params.faqcs.plus(params.shared), fastqFiles,avgLen)
+
         paired = FAQCS.out.paired.ifEmpty(params.pairedFiles)
         unpaired = FAQCS.out.unpaired.ifEmpty(params.unpairedFiles)
     }

modules/runFaQCs/runFaQCs.nf

@@ -1,6 +1,5 @@
 #!/usr/bin/env nextflow
 
-
 //double-checks that any provided adapter file is in FASTA format
 process adapterFileCheck {
     label "qc"

modules/sra2fastq/sra2fastq.nf

@@ -10,6 +10,7 @@ process sraDownload {
     publishDir "${settings["outDir"]}/SRA_Download", mode: 'copy'
 
     //retries download in case of transient failure, then completes any downloads that didn't fail
+
     maxRetries 3
     errorStrategy { (task.attempt <= maxRetries) ? 'retry' : 'finish' }
 
@@ -49,4 +50,5 @@ workflow SRA2FASTQ {
 
     emit:
     fastq
+
 }

nextflow.config

@@ -24,6 +24,7 @@ params {
 
     sra2fastq {
         clean = false
+
         accessions = []
     }
 
@@ -39,6 +40,7 @@ params {
         numN = 2
         filtLC = 0.85
         filtPhiX = false
+
     }
 
     hostRemoval {
@@ -139,6 +141,6 @@ executor {
     submitRateLimit = '1/5sec'
 }
 
-
 //cleanup
-cleanup = true
+cleanup = false
+

runAntiSmash/Dockerfile

@@ -0,0 +1,7 @@
+# syntax=docker/dockerfile:1
+FROM antismash/standalone-lite-nonfree:7.1.0
+
+#we override the base image's entrypoint for appropriate interaction with Nextflow
+ENTRYPOINT ["/usr/bin/env"]
+SHELL ["/bin/bash", "-c"]
+CMD /bin/bash

runAntiSmash/nextflow.config

@@ -0,0 +1,29 @@
+params {
+    //defaults
+    input = null //either contig file or gbk from annotation
+    projName = "Project"
+    outDir = "."
+    numCPU=8
+    database = "$projectDir/../../database/antiSMASH" //path to downloaded database location (download-antismash-databases --database-dir <DBPATH>)
+    //defaults
+    taxon = 'bacteria'
+    clusterblast = false
+    subclusterblast = true
+    knownclusterblast = true
+    mibig = false
+    smcogs = false
+    pfam2go = false
+    asf = true
+    rre = true
+    fullhmm = false
+    tigrfam = false
+    cassis = false //only with fungi
+}
+
+process.container="apwat/sma:0.14"
+singularity{
+    enabled=true
+    runOptions="--compat -H $PWD --bind $projectDir/../../database/antiSMASH:$projectDir/../../database/antiSMASH"
+}
+
+cleanup=true

runAntiSmash/runAntiSmash.nf

@@ -0,0 +1,55 @@
+
+//runs ANTISMASH on provided .fa or .gbk input.
+process antismash {
+    publishDir(
+        path: "$params.outDir/AssemblyBasedAnalysis/AntiSmash",
+        mode: 'copy'
+    )
+
+    input:
+    path input
+
+    output:
+    path "output/*"
+    path "antismashLog.txt"
+
+    script:
+    def taxon = params.taxon.equalsIgnoreCase("fungi") ? "--taxon fungi" : "--taxon bacteria"
+    def clusterblast = params.clusterblast == true ? "--cb-general" : ""
+    def subclusterblast = params.subclusterblast == true ? "--cb-subclusters" : ""
+    def knownclusterblast = params.knownclusterblast == true ? "--cb-knownclusters" : ""
+    def mibig = params.mibig == true ? "--cc-mibig" : ""
+    def smcogs = params.smcogs == true ? "--smcog-trees" : ""
+    def asf = params.asf == true ? "--asf" : ""
+    def rre = params.rre == true ? "--rre" : ""
+    def fullhmmer = params.fullhmm == true ? "--fullhmmer" : ""
+    def tigrfam = params.tigrfam == true ? "--tigrfam" : ""
+    def pfam2go = params.pfam2go == true ? "--pfam2go" : ""
+    def genefinding = params.taxon.equalsIgnoreCase("fungi") ? "--genefinding-tool glimmerhmm" : "--genefinding-tool prodigal-m"
+    def cassis = (params.taxon.equalsIgnoreCase("fungi") && params.cassis == true) ? "--cassis" : ""
+
+    """
+    antismash -c $params.numCPU $taxon \
+    --logfile antismashLog.txt --output-dir ./output \
+    --html-title $params.projName --database $params.database \
+    $clusterblast \
+    $subclusterblast \
+    $knownclusterblast \
+    $mibig \
+    $smcogs \
+    $asf \
+    $rre \
+    $fullhmmer \
+    $tigrfam \
+    $pfam2go \
+    $cassis \
+    $genefinding \
+    $input
+    """
+
+}
+
+
+workflow {
+    antismash(channel.fromPath(params.input,checkIfExists:true))
+}

runAntiSmash/test_files/parameters/antismash_all_opts.json

@@ -0,0 +1,16 @@
+{
+    "numCPU": 4,
+    "input": "${projectDir}/../test_data/contigs.fa",
+    "projName": "BasicAntismashTest",
+    "database": "${projectDir}/../../database/antiSMASH",
+    "clusterblast": true,
+    "subclusterblast": true,
+    "knownclusterblast": true,
+    "mibig": true,
+    "smcogs": true,
+    "pfam2go": true,
+    "asf": true,
+    "rre": true,
+    "fullhmm": true,
+    "tigrfam": true
+}

runAntiSmash/test_files/parameters/antismash_basic.json

@@ -0,0 +1,6 @@
+{
+    "numCPU": 4,
+    "input": "${projectDir}/../test_data/contigs.fa",
+    "projName": "BasicAntismashTest",
+    "database": "${projectDir}/../../database/antiSMASH"
+}

runAntiSmash/test_files/parameters/antismash_fungi.json

@@ -0,0 +1,8 @@
+{
+    "numCPU": 4,
+    "input": "${projectDir}/../test_data/contigs.fa",
+    "projName": "FungiAntismashTest",
+    "database": "${projectDir}/../../database/antiSMASH",
+    "taxon": "fungi",
+    "cassis": true
+}

tests/modules/countFastq/countFastq.nf.test

@@ -57,6 +57,4 @@ nextflow_workflow {
         }
 
     }
-
-
 }

tests/modules/countFastq/countFastq.nf.test.snap

@@ -27,6 +27,7 @@
             "nextflow": "24.10.3"
         },
         "timestamp": "2025-01-06T13:53:45.128251613"
+
     },
     "1 Unpaired File": {
         "content": [
@@ -35,12 +36,14 @@
                     "151"
                 ],
                 "1": [
+
                     "all.se.fastq:md5,c9cd5b2586c75c7448674ff3ff5451de"
                 ],
                 "avgReadLen": [
                     "151"
                 ],
                 "fastqFiles": [
+
                     "all.se.fastq:md5,c9cd5b2586c75c7448674ff3ff5451de"
                 ]
             }

tests/modules/runFaQCs/runFaQCs.nf.test.snap

@@ -13,6 +13,7 @@
                         "QC.1.trimmed.fastq:md5,deb773f1726c6134a7d2fc069af7b21b",
                         "QC.2.trimmed.fastq:md5,a793e8ccfe60c0f9462a80d520eecd7a"
                     ]
+
                 ]
             }
         ],
@@ -21,6 +22,7 @@
             "nextflow": "24.10.3"
         },
         "timestamp": "2025-01-06T14:15:19.062459705"
+
     },
     "Basic SE": {
         "content": [
@@ -30,6 +32,7 @@
                 ],
                 "trimmed": [
                     "QC.unpaired.trimmed.fastq:md5,3a0138c06e9cd504e2cca8e5d93532f1"
+
                 ]
             }
         ],
@@ -38,6 +41,7 @@
             "nextflow": "24.10.3"
         },
         "timestamp": "2025-01-06T14:14:24.933787665"
+
     },
     "SE with adapter removal": {
         "content": [
@@ -47,6 +51,7 @@
                 ],
                 "trimmed": [
                     "QC.unpaired.trimmed.fastq:md5,3e43d37648eea875f5583f5cfcbb16ca"
+
                 ]
             }
         ],
@@ -55,6 +60,7 @@
             "nextflow": "24.10.3"
         },
         "timestamp": "2025-01-06T14:15:03.845678151"
+
     },
     "Basic PE": {
         "content": [
@@ -70,6 +76,7 @@
                         "QC.1.trimmed.fastq:md5,deb773f1726c6134a7d2fc069af7b21b",
                         "QC.2.trimmed.fastq:md5,a793e8ccfe60c0f9462a80d520eecd7a"
                     ]
+
                 ]
             }
         ],
@@ -78,6 +85,7 @@
             "nextflow": "24.10.3"
         },
         "timestamp": "2025-01-06T14:14:13.196766924"
+
     },
     "PE with adapter removal": {
         "content": [
@@ -93,6 +101,7 @@
                         "QC.1.trimmed.fastq:md5,1e70223f29baaced4509b62a5e84f074",
                         "QC.2.trimmed.fastq:md5,649bf376592b80e9ae1cee81d018a65f"
                     ]
+
                 ]
             }
         ],

tests/modules/sra2fastq/sra2fastq.nf.test

@@ -91,5 +91,4 @@ nextflow_workflow {
         }
 
     }
-
 }

tests/modules/sra2fastq/sra2fastq.nf.test.snap

@@ -23,6 +23,7 @@
                     "SRR29462562.fastq.gz:md5,31506ee0f339cb6398dd326d5cb23b77"
                 ],
                 "fastq": [
+
                     "SRR29462562.fastq.gz:md5,31506ee0f339cb6398dd326d5cb23b77"
                 ]
             }
@@ -48,6 +49,5 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-01-06T14:20:03.994730963"
     }
 }

tests/nextflow.config

@@ -4,4 +4,5 @@
 ========================================================================================
 */
 
-cleanup = false //necessary to compare snapshotted files
+cleanup = false //necessary to compare snapshotted files
+