stub ready and working

modules/checkV.nf

@@ -15,4 +15,10 @@ process checkV {
         checkv quality_summary ${fasta}  results #2> /dev/null
         cp results/quality_summary.tsv ${name}_quality_summary.tsv #2> /dev/null
         """
+    stub:
+        """
+        mkdir negative_result_${name}.txt
+        echo "contig_id	contig_length	genome_copies	gene_count	viral_genes	host_genes	checkv_quality	miuvig_quality	completeness	completeness_method	contamination	provirus	termini	warnings" > ${name}_quality_summary.tsv
+        echo "pos_phage_0	146647	1.0	243	141	1	High-quality	High-quality	97.03	AAI-based	0.0	No" >> ${name}_quality_summary.tsv   
+        """
 }

modules/chromomap.nf

@@ -83,4 +83,11 @@ process chromomap {
       """
       echo "nothing found" > sample_overview_${type}.html
       """
+      stub:
+        """
+        touch sample_overview_${type}.html
+        """
 }
+
+
+

modules/databases/download_checkV_DB.nf

@@ -11,4 +11,8 @@ process download_checkV_DB {
         tar -zxvf checkv-db-v0.6.tar.gz
         rm checkv-db-v0.6.tar.gz
         """
+    stub:
+        """
+        mkdir checkv-db-v0.6
+        """
 }

modules/databases/download_pvog_DB.nf

@@ -9,6 +9,10 @@ process pvog_DB {
         wget -nH ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/viral-pipeline/hmmer_databases/pvogs.tar.gz && tar -zxvf pvogs.tar.gz
         rm pvogs.tar.gz
         """
+    stub:
+        """
+        mkdir pvogs
+        """
 }
 
 process vogtable_DB {
@@ -21,6 +25,10 @@ process vogtable_DB {
         """
         wget -nH http://dmk-brain.ecn.uiowa.edu/pVOGs/downloads/VOGTable.txt
         """
+    stub:
+        """
+        touch VOGTable.txt
+        """
 }
 
 /*

modules/databases/download_references.nf

@@ -9,4 +9,8 @@ process download_references {
         git clone -b WtP-v0.9 https://github.com/mult1fractal/WtP_phage_reference_db-WtP_v0.9.0.git
         cat WtP_phage_reference_db-WtP_v0.9.0/fasta-files/*.fa > phage_references.fa
         """
+    stub:
+        """
+        touch phage_references.fa
+        """        
 }

modules/databases/phage_references_blastDB.nf

@@ -14,6 +14,11 @@ process phage_references_blastDB {
         mkdir phage_blast_DB && mv phage_db.* phage_blast_DB
         tar czf blast_database.tar.gz phage_blast_DB/
         """
+    stub:
+        """
+        mkdir phage_blast_DB
+        tar czf blast_database.tar.gz phage_blast_DB/
+        """        
 }
 
 //phage_blast_DB/phage_db.*

modules/databases/ppr_download_dependencies.nf

@@ -8,4 +8,8 @@ process ppr_download_dependencies {
         """
         git clone https://github.com/Stormrider935/PPR-Meta.git
         """
+    stub:
+        """
+        mkdir PPR-Meta
+        """        
 }

modules/databases/sourmash_download_DB.nf

@@ -3,12 +3,16 @@ process sourmash_download_DB {
     else { storeDir "${params.databases}/sourmash/" }
     label 'sourmash' 
     input:
-        file(references)
+        path(references)
     output:
-        file("phages.sbt.zip")
+        path("phages.sbt.zip")
     script:
         """
         sourmash compute --scaled 100 -k 21 --singleton --seed 42 -p 8 -o phages.sig ${references}
         sourmash index phages.sbt.zip phages.sig
         """
+    stub:
+        """
+        touch phages.sbt.zip
+        """
 }

modules/databases/vibrant_download_DB.nf

@@ -15,6 +15,11 @@ process vibrant_download_DB {
         cp /opt/conda/share/vibrant-1.0.1/files/VIBRANT*.{tsv,sav} database
         tar -czf database.tar.gz database/
         """
+    stub:
+        """
+        mkdir database
+        tar -czf database.tar.gz database/
+        """
 }
 
 

modules/databases/virsorter2_download_DB.nf

@@ -11,5 +11,9 @@ process virsorter2_download_DB {
         chmod -R a+rX db
         rm db.tgz
         """
+    stub:
+        """
+        mkdir db
+        """
 }
 

modules/databases/virsorter_download_DB.nf

@@ -10,6 +10,10 @@ process virsorter_download_DB {
         tar -xvzf virsorter-data-v2.tar.gz
         rm virsorter-data-v2.tar.gz
         """
+    stub:
+        """
+        mkdir virsorter-data
+        """
 }
 
 

modules/hmmscan.nf

@@ -10,6 +10,10 @@ process hmmscan {
         """
         hmmscan --cpu ${task.cpus} ${params.hmm_params} --noali --domtblout ${name}_${pvog_db}_hmmscan.tbl ${pvog_db}/${pvog_db}.hmm ${faa}
         """
+    stub:
+        """
+        touch ${name}_${pvog_db}_hmmscan.tbl
+        """
 }
 
 

modules/hue_heatmap.nf

@@ -10,4 +10,8 @@ process hue_heatmap {
         """
         hue_heatmap_plot.py --input *.tsv --output ${name}_phage-distribution.pdf
         """
+      stub:
+        """
+        touch ${name}_phage-distribution.pdf   
+        """        
 }

modules/input_suffix_check.nf

@@ -1,9 +1,9 @@
 process input_suffix_check {
     label 'ubuntu'
     input:
-        tuple val(name), file(file) 
+        tuple val(name), path(file) 
     output:
-        tuple val(name), file("${name}.fa")
+        tuple val(name), path("${name}.fa")
     script:
         """
         case "${file}" in
@@ -32,6 +32,10 @@ process input_suffix_check {
         # remove empty lines
         sed '/^\$/d' -i ${name}.fa
         """
+    stub:
+        """
+        touch ${name}.fa
+        """
 }
 
 

modules/normalize_contig_size.nf

@@ -8,5 +8,9 @@ process normalize_contig_size {
         """
         cut.py --size 3000 --genome ${fasta} --outfile ${name}_fragments.fasta
         """
+    stub:
+        """
+        touch ${name}_fragments.fasta
+        """
 }
 

modules/parser/chromomap_parser.nf

@@ -24,4 +24,15 @@ process chromomap_parser {
             grep --no-messages -w "\$f1" annotationfile.tbl 1>> small/annotationfile.tbl || true
         done < small/chromosomefile.tbl
         """
+      stub:
+        """
+        mkdir small
+        mkdir large
+
+        touch small/chromosomefile.tbl
+        touch small/annotationfile.tbl
+
+        touch large/chromosomefile.tbl
+        touch large/annotationfile.tbl
+        """
 }

modules/parser/filter_virnet.nf

@@ -13,4 +13,8 @@ process filter_virnet {
         # extract correct positive contigs
         parse_virnet.py --input all_virnet_results.txt --output virnet_\${PWD##*/}.tsv
         """
+    stub:
+        """
+        mkdir touch virnet_\${PWD##*/}.tsv
+        """
 }

modules/prodigal.nf

@@ -9,4 +9,8 @@ process prodigal {
         """
         prodigal -p "meta" -a ${name}_prodigal.faa -i ${positive_contigs}
         """
+    stub:
+        """
+        touch ${name}_prodigal.faa
+        """
 }

modules/raw_data_collection/deepvirfinder_collect_data.nf

@@ -12,4 +12,9 @@ process deepvirfinder_collect_data {
         tail -q -n+2 ${output_lists} >> deepvirfinder/${name}_overview.txt
         tar -czf deepvirfinder_results_${name}.tar.gz deepvirfinder
         """
+    stub:
+        """
+        mkdir deepvirfinder
+        tar -czf deepvirfinder_results_${name}.tar.gz deepvirfinder
+        """
 }

modules/raw_data_collection/metaphinder_collect_data.nf

@@ -2,9 +2,9 @@ process metaphinder_collect_data {
     publishDir "${params.output}/${name}/raw_data", mode: 'copy', pattern: "metaphinder_results_${name}.tar.gz"
     label 'ubuntu'
     input:
-        tuple val(name), file(output_lists), file(output_blasts)
+        tuple val(name), path(output_lists), path(output_blasts)
     output:
-        tuple val(name), file("metaphinder_results_${name}.tar.gz")
+        tuple val(name), path("metaphinder_results_${name}.tar.gz")
     script:
         """
         mkdir -p metaphinder/blast_results
@@ -13,15 +13,20 @@ process metaphinder_collect_data {
         cp ${output_blasts} metaphinder/blast_results
         tar -czf metaphinder_results_${name}.tar.gz metaphinder
         """
+    stub:
+        """
+        mkdir metaphinder
+        tar -czf metaphinder_results_${name}.tar.gz metaphinder
+        """
 }
 
 process metaphinder_collect_data_ownDB {
     publishDir "${params.output}/${name}/raw_data", mode: 'copy', pattern: "metaphinder_ownDB_results_${name}.tar.gz"
     label 'ubuntu'
     input:
-        tuple val(name), file(output_lists), file(output_blasts)
+        tuple val(name), path(output_lists), path(output_blasts)
     output:
-        tuple val(name), file("metaphinder_ownDB_results_${name}.tar.gz")
+        tuple val(name), path("metaphinder_ownDB_results_${name}.tar.gz")
     script:
         """
         mkdir -p metaphinder_ownDB/blast_results
@@ -30,4 +35,9 @@ process metaphinder_collect_data_ownDB {
         cp ${output_blasts} metaphinder_ownDB/blast_results
         tar -czf metaphinder_ownDB_results_${name}.tar.gz metaphinder_ownDB
         """
+    stub:
+        """
+        mkdir metaphinder_ownDB
+        tar -czf metaphinder_ownDB_results_${name}.tar.gz metaphinder_ownDB
+        """
 }

modules/raw_data_collection/phigaro_collect_data.nf

@@ -11,4 +11,9 @@ process phigaro_collect_data {
         cp -r ${rawdir}/* phigaro
         tar -czf phigaro_results_${name}.tar.gz phigaro
         """
+    stub:
+        """
+        mkdir phigaro
+        tar -czf phigaro_results_${name}.tar.gz phigaro
+        """
 }

modules/raw_data_collection/pprmeta_collect_data.nf

@@ -2,13 +2,18 @@ process pprmeta_collect_data {
     publishDir "${params.output}/${name}/raw_data", mode: 'copy', pattern: "pprmeta_results_${name}.tar.gz"
     label 'ubuntu'
     input:
-        tuple val(name), file(output_lists)
+        tuple val(name), path(output_lists)
     output:
-        tuple val(name), file("pprmeta_results_${name}.tar.gz")
+        tuple val(name), path("pprmeta_results_${name}.tar.gz")
     script:
         """
         cat ${output_lists} | head -1 > ${name}_overview.txt
         tail -q -n+2 ${output_lists} >> ${name}_overview.txt
         tar -czf pprmeta_results_${name}.tar.gz ${name}_overview.txt
         """
+    stub:
+        """
+        touch ${name}_overview.txt
+        tar -czf pprmeta_results_${name}.tar.gz ${name}_overview.txt
+        """
 }

modules/raw_data_collection/sourmash_collect_data.nf

@@ -2,13 +2,18 @@ process sourmash_collect_data {
     publishDir "${params.output}/${name}/raw_data", mode: 'copy', pattern: "sourmash_results_${name}.tar.gz"
     label 'ubuntu'
     input:
-        tuple val(name), file(output_lists)
+        tuple val(name), path(output_lists)
     output:
-        tuple val(name), file("sourmash_results_${name}.tar.gz")
+        tuple val(name), path("sourmash_results_${name}.tar.gz")
     script:
         """
         echo "similarity,name,filename,md5" > ${name}_overview.txt
         tail -q -n +2 ${output_lists} >> ${name}_overview.txt
         tar -czf sourmash_results_${name}.tar.gz ${name}_overview.txt
         """
+    stub:
+        """
+        touch ${name}_overview.txt
+        tar -czf sourmash_results_${name}.tar.gz ${name}_overview.txt
+        """
 }

modules/raw_data_collection/vibrant_collect_data.nf

@@ -2,9 +2,9 @@ process vibrant_collect_data {
     publishDir "${params.output}/${name}/raw_data", mode: 'copy', pattern: "vibrant_results_${name}.tar.gz"
     label 'ubuntu'
     input:
-        tuple val(name), file(output_lists), file(dirs)
+        tuple val(name), path(output_lists), path(dirs)
     output:
-        tuple val(name), file("vibrant_results_${name}.tar.gz")
+        tuple val(name), path("vibrant_results_${name}.tar.gz")
     script:
         """
         mkdir -p vibrant/results
@@ -13,16 +13,21 @@ process vibrant_collect_data {
         tail -q -n +2 ${output_lists} >> vibrant/${name}_overview.txt
         tar -czf vibrant_results_${name}.tar.gz vibrant
         """
+    stub:
+        """
+        mkdir vibrant
+        tar -czf vibrant_results_${name}.tar.gz vibrant
+        """
 }
 
 
 process vibrant_virome_collect_data {
     publishDir "${params.output}/${name}/raw_data", mode: 'copy', pattern: "vibrant_virome_results_${name}.tar.gz"
     label 'ubuntu'
     input:
-        tuple val(name), file(output_lists), file(dirs)
+        tuple val(name), path(output_lists), path(dirs)
     output:
-        tuple val(name), file("vibrant_virome_results_${name}.tar.gz")
+        tuple val(name), path("vibrant_virome_results_${name}.tar.gz")
     script:
         """
         mkdir -p vibrant/results
@@ -31,4 +36,9 @@ process vibrant_virome_collect_data {
         tail -q -n +2 ${output_lists} >> vibrant/${name}_overview.txt
         tar -czf vibrant_virome_results_${name}.tar.gz vibrant
         """
+    stub:
+        """
+        mkdir vibrant
+        tar -czf vibrant_virome_results_${name}.tar.gz vibrant
+        """
 }

modules/raw_data_collection/virfinder_collect_data.nf

@@ -11,4 +11,9 @@ process virfinder_collect_data {
         cp ${output_lists} virfinder
         tar -czf virfinder_results_${name}.tar.gz virfinder
         """
+    stub:
+        """
+        mkdir virfinder
+        tar -czf virfinder_results_${name}.tar.gz virfinder
+        """
 }