From cee4b6f3cd7abaacefc9d3c6d640ab293f7c3724 Mon Sep 17 00:00:00 2001
From: MarieLataretu <marie.lataretu@uni-jena.de>
Date: Mon, 18 Jan 2021 12:28:31 +0100
Subject: [PATCH] not the latest report in output/Logs Fixes #126

---
 bin/reports.sh  | 11 -----------
 main.nf         | 10 +---------
 nextflow.config |  8 +++-----
 3 files changed, 4 insertions(+), 25 deletions(-)
 delete mode 100755 bin/reports.sh

diff --git a/bin/reports.sh b/bin/reports.sh
deleted file mode 100755
index 2ce3da6..0000000
--- a/bin/reports.sh
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/usr/bin/bash
-
-# copy final reports to output dir
-
-OUTPUT_DIR=$1
-REPORTS_DIR=$2
-
-mkdir -p $OUTPUT_DIR/Logs
-
-cp $REPORTS_DIR/execution_report.html $OUTPUT_DIR/Logs
-cp $REPORTS_DIR/execution_timeline.html $OUTPUT_DIR/Logs
diff --git a/main.nf b/main.nf
index 33a3035..5bee532 100755
--- a/main.nf
+++ b/main.nf
@@ -24,7 +24,7 @@ nextflow.enable.dsl=2
 
 // Parameters sanity checking
 
-Set valid_params = ['max_cores', 'cores', 'memory', 'profile', 'help', 'reads', 'genome', 'annotation', 'deg', 'autodownload', 'pathway', 'species', 'include_species', 'strand', 'mode', 'tpm', 'fastp_additional_params', 'hisat2_additional_params', 'featurecounts_additional_params', 'feature_id_type', 'busco_db', 'dammit_uniref90', 'skip_sortmerna', 'assembly', 'output', 'fastp_dir', 'sortmerna_dir', 'hisat2_dir', 'featurecounts_dir', 'tpm_filter_dir', 'annotation_dir', 'deseq2_dir', 'assembly_dir', 'rnaseq_annotation_dir', 'uniref90_dir', 'multiqc_dir', 'permanentCacheDir', 'condaCacheDir', 'singularityCacheDir', 'softlink_results', 'runinfo', 'cloudProcess', 'permanent-cache-dir', 'conda-cache-dir', 'singularity-cache-dir', 'cloud-process'] // don't ask me why there is 'permanent-cache-dir', 'conda-cache-dir', 'singularity-cache-dir', 'cloud-process'
+Set valid_params = ['max_cores', 'cores', 'memory', 'profile', 'help', 'reads', 'genome', 'annotation', 'deg', 'autodownload', 'pathway', 'species', 'include_species', 'strand', 'mode', 'tpm', 'fastp_additional_params', 'hisat2_additional_params', 'featurecounts_additional_params', 'feature_id_type', 'busco_db', 'dammit_uniref90', 'skip_sortmerna', 'assembly', 'output', 'fastp_dir', 'sortmerna_dir', 'hisat2_dir', 'featurecounts_dir', 'tpm_filter_dir', 'annotation_dir', 'deseq2_dir', 'assembly_dir', 'rnaseq_annotation_dir', 'uniref90_dir', 'multiqc_dir', 'nf_runinfo_dir', 'permanentCacheDir', 'condaCacheDir', 'singularityCacheDir', 'softlink_results', 'cloudProcess', 'permanent-cache-dir', 'conda-cache-dir', 'singularity-cache-dir', 'cloud-process'] // don't ask me why there is 'permanent-cache-dir', 'conda-cache-dir', 'singularity-cache-dir', 'cloud-process'
 def parameter_diff = params.keySet() - valid_params
 if (parameter_diff.size() != 0){
     exit 1, "ERROR: Parameter(s) $parameter_diff is/are not valid in the pipeline!\n"
@@ -726,14 +726,6 @@ workflow {
     }
 }
 
-
-workflow.onComplete { 
-    if (workflow.success) {
-        // copy execution and timeline HTML reports to output dir
-        println (['bash', "${workflow.projectDir}/bin/reports.sh", "${params.output}", "${params.runinfo}"].execute().text)
-    }
-}
-
 def helpMSG() {
     c_green = "\033[0;32m";
     c_reset = "\033[0m";
diff --git a/nextflow.config b/nextflow.config
index f8b5d7f..8ade6e2 100755
--- a/nextflow.config
+++ b/nextflow.config
@@ -56,6 +56,7 @@ params {
     // if the UniRef90 option for dammit is activated via --dammit_uniref90, this parameter will be set to 'uniref90' for the dammit output 
     uniref90_dir = '' 
     multiqc_dir = 'Summary'
+    nf_runinfo_dir = 'Logs'
 
     // location for autodownload data like databases
     permanentCacheDir = 'nextflow-autodownload-databases'
@@ -67,21 +68,18 @@ params {
     // softlink results instead of copying
     softlink_results = false
 
-    // save execution information
-    runinfo = "nextflow-run-infos"
-
     cloudProcess = false
 }
 
 
 timeline {
   enabled = true
-  file = "${params.runinfo}/execution_timeline.html"
+  file = "${params.output}/${params.nf_runinfo_dir}/execution_timeline.html"
 }
 
 report {
   enabled = true
-  file = "${params.runinfo}/execution_report.html"
+  file = "${params.output}/${params.nf_runinfo_dir}/execution_report.html"
 }
 
 profiles {