add nextflow.config

nextflow.config

@@ -0,0 +1,73 @@
+/*
+ * -------------------------------------------------
+ * Nextflow config file for clockwork
+ * -------------------------------------------------
+ *
+ */
+
+
+manifest {
+  author = 'Martin Hunt et al'
+  description = 'Pipelines for processing bacterial sequence data (Illumina only) and variant calling'
+  homePage = 'https://github.com/iqbal-lab-org/clockwork'
+  name = 'clockwork'
+  nextflowVersion = '>=19.07.0'
+  version = '0.8.0'
+}
+
+params {
+  cortex_mem_height = 22
+  dataset_name = "" 
+  db_config_file = "" 
+  dropbox_dir = ""
+  help = false
+  max_forks  = 20  // also listed as 100, https://github.com/iqbal-lab-org/clockwork/blob/master/nextflow/generic_pipeline.nf#L6
+  max_forks_combine_variant_calls = 100
+  max_forks_cortex = 100
+  max_forks_fastqc = 100 
+  max_forks_map_reads = 100 
+  max_forks_sam_to_fastq_files = 100
+  max_forks_samtools = 100
+  max_forks_samtools_qc = 100
+  max_forks_trim_reads = 100 
+  max_ram = 4
+  minos_max_read_length = 200
+  outprefix = ""
+  output_dir = "" 
+  pipeline_name = ""
+  pipeline_root  = ""
+  reads_in1 = "" 
+  reads_in2 = "" 
+  ref_dir = "" 
+  ref_fasta = ""
+  ref_id = "" 
+  ref_metadata_tsv = ""
+  references_root = "" 
+  sample_name = ""
+  script = "" 
+  testing = false
+  truth_ref = "" 
+  xlsx_archive_dir = ""
+}
+
+
+trace {
+    enabled = true
+    file = 'trace.txt'
+    fields = 'task_id,hash,native_id,process,tag,name,status,exit,module,container,cpus,time,disk,memory,attempt,submit,start,complete,duration,realtime,queue,%cpu,%mem,rss,vmem,peak_rss,peak_vmem,rchar,wchar,syscr,syscw,read_bytes,write_bytes'
+}
+
+timeline {
+    enabled = true
+    file = 'timeline.html'
+}
+
+report {
+    enabled = true
+    file = 'report.html'
+}
+
+dag {
+    enabled = false
+    file = 'dag.pdf'
+}

nextflow/fake_remove_contam.nf

@@ -1,9 +1,4 @@
-params.help = false
-params.pipeline_root = ""
-params.db_config_file = ""
-params.dataset_name = ""
-params.max_forks = 20
-
+#!/usr/bin/env nextflow
 
 if (params.help){
     log.info"""

nextflow/generic_pipeline.nf

@@ -1,12 +1,4 @@
-params.help = false
-params.pipeline_root = ""
-params.db_config_file = ""
-params.dataset_name = ""
-params.script = ""
-params.max_forks = 100
-params.max_ram = 4
-params.pipeline_name = ""
-
+#!/usr/bin/env nextflow
 
 if (params.help){
     log.info"""

nextflow/import.nf

@@ -1,9 +1,4 @@
-params.help = false
-params.dropbox_dir = ""
-params.pipeline_root = ""
-params.db_config_file = ""
-params.xlsx_archive_dir = ""
-
+#!/usr/bin/env nextflow
 
 if (params.help){
     log.info"""

nextflow/mykrobe_predict.nf

@@ -1,10 +1,4 @@
-params.help = false
-params.ref_id = ""
-params.references_root = ""
-params.pipeline_root = ""
-params.db_config_file = ""
-params.dataset_name = ""
-params.testing = false
+#!/usr/bin/env nextflow
 
 if (params.testing) {
     test_opt_string = '--testing'

nextflow/qc.nf

@@ -1,16 +1,4 @@
-params.help = false
-params.ref_id = ""
-params.references_root = ""
-params.pipeline_root = ""
-params.db_config_file = ""
-params.dataset_name = ""
-params.ref_fasta = ""
-params.reads_in1 = ""
-params.reads_in2 = ""
-params.output_dir = ""
-params.max_forks_samtools_qc = 100
-params.max_forks_fastqc = 100
-
+#!/usr/bin/env nextflow
 
 if (params.help){
     log.info"""

nextflow/remove_contam.nf

@@ -1,18 +1,4 @@
-params.help = false
-params.reads_in1 = ""
-params.reads_in2 = ""
-params.outprefix = ""
-params.ref_metadata_tsv = ""
-params.pipeline_root = ""
-params.references_root = ""
-params.db_config_file = ""
-params.dataset_name = ""
-params.ref_fasta = ""
-params.ref_id = ""
-params.testing = false
-params.max_forks_map_reads = 100
-params.max_forks_sam_to_fastq_files = 100
-
+#!/usr/bin/env nextflow
 
 if (params.help){
     log.info"""

nextflow/variant_call.nf

@@ -1,24 +1,4 @@
-params.help = false
-params.ref_id = ""
-params.references_root = ""
-params.pipeline_root = ""
-params.db_config_file = ""
-params.dataset_name = ""
-params.ref_dir = ""
-params.reads_in1 = ""
-params.reads_in2 = ""
-params.output_dir = ""
-params.sample_name = ""
-params.testing = false
-params.cortex_mem_height = 22
-params.max_forks_trim_reads = 100
-params.max_forks_map_reads = 100
-params.max_forks_samtools = 100
-params.max_forks_cortex = 100
-params.max_forks_combine_variant_calls = 100
-params.minos_max_read_length = 200
-params.truth_ref = ""
-
+#!/usr/bin/env nextflow
 
 if (params.help){
     log.info"""