From a67507a0e11cacaab963b8b4cd2b7b9ad41c6b14 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Sat, 7 Nov 2020 07:06:42 +0100
Subject: [PATCH] Bring standard summary log messages in line with template
---
main.nf | 31 ++++++++++++-------------------
1 file changed, 12 insertions(+), 19 deletions(-)
diff --git a/main.nf b/main.nf
index 3528a41..1e48420 100644
--- a/main.nf
+++ b/main.nf
@@ -36,7 +36,7 @@ def helpMessage() {
Alignments
--split_fastq [bool] Split fastq files in reads chunks to speed up computation. Default: false
--fastq_chunks_size [int] Size of read chunks if split_fastq is true. Default: 20000000
- --save_aligned_intermediates [bool] Save intermediates alignment files. Default: False
+ --save_aligned_intermediates [bool] Save intermediates alignment files. Default: False
--bwt2_opts_end2end [str] Options for bowtie2 end-to-end mappinf (first mapping step). See hic.config for default.
--bwt2_opts_trimmed [str] Options for bowtie2 mapping after ligation site trimming. See hic.config for default.
--min_mapq [int] Minimum mapping quality values to consider. Default: 10
@@ -45,7 +45,7 @@ def helpMessage() {
--rm_singleton [bool] Remove singleton reads. Default: true
--rm_multi [bool] Remove multi-mapped reads. Default: true
--rm_dup [bool] Remove duplicates. Default: true
-
+
Contacts calling
--min_restriction_fragment_size [int] Minimum size of restriction fragments to consider. Default: 0
--max_restriction_fragment_size [int] Maximum size of restriction fragments to consider. Default: 0
@@ -189,7 +189,7 @@ else if ( params.fasta ) {
lastPath = params.fasta.lastIndexOf(File.separator)
fasta_base = params.fasta.substring(lastPath+1)
bwt2_base = fasta_base.toString() - ~/(\.fa)?(\.fasta)?(\.fas)?(\.fsa)?$/
-
+
Channel.fromPath( params.fasta )
.ifEmpty { exit 1, "Genome index: Fasta file not found: ${params.fasta}" }
.set { fasta_for_index }
@@ -255,24 +255,17 @@ summary['Min Insert Size'] = params.min_insert_size
summary['Max Insert Size'] = params.max_insert_size
summary['Min CIS dist'] = params.min_cis_dist
summary['Maps resolution'] = params.bin_size
-summary['Max Memory'] = params.max_memory
-summary['Max CPUs'] = params.max_cpus
-summary['Max Time'] = params.max_time
+summary['Max Resources'] = "$params.max_memory memory, $params.max_cpus cpus, $params.max_time time per job"
+if (workflow.containerEngine) summary['Container'] = "$workflow.containerEngine - $workflow.container"
summary['Output dir'] = params.outdir
+summary['Launch dir'] = workflow.launchDir
summary['Working dir'] = workflow.workDir
-summary['Container Engine'] = workflow.containerEngine
-if(workflow.containerEngine)
- summary['Container'] = workflow.container
-summary['Current home'] = "$HOME"
-summary['Current user'] = "$USER"
-summary['Current path'] = "$PWD"
-summary['Working dir'] = workflow.workDir
-summary['Output dir'] = params.outdir
summary['Script dir'] = workflow.projectDir
-summary['Config Profile'] = workflow.profile
-if(workflow.profile == 'awsbatch'){
- summary['AWS Region'] = params.awsregion
- summary['AWS Queue'] = params.awsqueue
+summary['User'] = workflow.userName
+if (workflow.profile.contains('awsbatch')) {
+ summary['AWS Region'] = params.awsregion
+ summary['AWS Queue'] = params.awsqueue
+ summary['AWS CLI'] = params.awscli
}
summary['Config Profile'] = workflow.profile
if (params.config_profile_description) summary['Config Profile Description'] = params.config_profile_description
@@ -738,7 +731,7 @@ process remove_duplicates {
echo -n "valid_interaction_rmdup\t" >> stats/${sample}/${sample}_allValidPairs.mergestat
cat ${sample}.allValidPairs | wc -l >> stats/${sample}/${sample}_allValidPairs.mergestat
- ## Count short range (<20000) vs long range contacts
+ ## Count short range (<20000) vs long range contacts
awk 'BEGIN{cis=0;trans=0;sr=0;lr=0} \$2 == \$5{cis=cis+1; d=\$6>\$3?\$6-\$3:\$3-\$6; if (d<=20000){sr=sr+1}else{lr=lr+1}} \$2!=\$5{trans=trans+1}END{print "trans_interaction\\t"trans"\\ncis_interaction\\t"cis"\\ncis_shortRange\\t"sr"\\ncis_longRange\\t"lr}' ${sample}.allValidPairs >> stats/${sample}/${sample}_allValidPairs.mergestat
"""
}
--
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