Renamed channels and variables for cache

bin/print_report.R

-
+#!/usr/bin/env Rscript
 
 #########################################################################
 ##                                                                     ##

dev/test.config

@@ -21,13 +21,13 @@ env {
     //in_path="/mnt/c/Users/Gael/Documents/Git_projects/14985_loot/dataset"
     //in_path="/mnt/share/14985_loot/dataset/B2699/00_Rawdata"
     //in_path="/pasteur/zeus/projets/p01/BioIT/gmillot/14985_loot/dataset/B4985/3" // where initial fastq file is
-    in_path="/pasteur/zeus/projets/p01/BioIT/gmillot/14985_loot/dataset/" 
+    in_path="$baseDir/dataset/" 
     //in_path="/pasteur/zeus/projets/p01/BioIT/gmillot/14985_loot/dataset/B2699/00_Rawdata" // where initial fastq file is
     fastq_file="test.fastq2.gz" // fastq file name
     //fastq_file="4-4_S1_L001_R1_001.fastq.gz"
     //fastq_file="3-4_S1_L001_R1_001.fastq.gz"
     //primer_fasta="/mnt/c/Users/Gael/Documents/Git_projects/14985_loot/dataset/20200520_adapters_TruSeq_B2699_14985_CL.fasta"
-    primer_fasta="/pasteur/zeus/projets/p01/BioIT/gmillot/14985_loot/results/20200520_res_CL14985_newtrim_align/20200520_adapters_TruSeq_B2699_14985_CL.fasta" // list of primers used for the library and used by Alien trimmer to trim the raw reads
+    primer_fasta="$baseDir/dataset/20200520_adapters_TruSeq_B2699_14985_CL.fasta" // list of primers used for the library and used by Alien trimmer to trim the raw reads
     //primer_fasta="/mnt/share/14985_loot/results/20200520_res_CL14985_newtrim_align/20200520_adapters_TruSeq_B2699_14985_CL.fasta"
     //// end path and files
 
@@ -46,7 +46,7 @@ env {
     //// end fivep_filtering
     cutoff_nb=25 // reads of length cutoff_nb after trimming are removed
     //ref_path="/mnt/c/Users/Gael/Documents/Git_projects/14985_loot/dataset/coli_K12_MG1655_NC_000913.3_ORI_CENTERED/"
-    ref_path="/pasteur/zeus/projets/p01/BioIT/gmillot/reference_genomes/coli_K12_MG1655_NC_000913.3_ORI_CENTERED/" // path of the reference genome
+    ref_path="$baseDir/dataset/coli_K12_MG1655_NC_000913.3_ORI_CENTERED/" // path of the reference genome
     ref_file="Ecoli-K12-MG1655_ORI_CENTERED.fasta" // fasta file of the reference genome
     ori_coord="2320711 2320942" // [2320711, 2320942] // Ecoli centered coordinates
     ter_coord="4627368 4627400" //[4627368, 4627400] // Ecoli centered coordinates
@@ -67,7 +67,7 @@ env {
 //// must be also exported
 system_exec = 'slurm' // the system that runs the workflow. Either 'local' or 'slurm'
 //out_path="/mnt/c/Users/Gael/Desktop" // where the report file will be saved. Example report_path = '.' for where the main.nf run is executed or report_path = '/mnt/c/Users/Gael/Desktop' 
-out_path="/pasteur/zeus/projets/p01/BioIT/gmillot/14985_loot/results" // where the report file will be saved. Example report_path = '.' for where the main.nf run is executed or report_path = '/mnt/c/Users/Gael/Desktop' 
+out_path="$baseDir/results/" // where the report file will be saved. Example report_path = '.' for where the main.nf run is executed or report_path = '/mnt/c/Users/Gael/Desktop' 
 //// end must be also exported
 
 //// general variables

main.nf

@@ -26,6 +26,9 @@ config_file = file("${projectDir}/nextflow.config")
 log_file = file("${launchDir}/.nextflow.log")
 file_name = file("${in_path}/${fastq_file}").baseName
 ref_name = file("${ref_path}/${ref_file}").baseName
+primer = file(primer_fasta)
+ref = file("${ref_path}/${ref_file}")
+sum_of_2_nb = fivep_seq_nb.toInteger()+added_nb.toInteger()
 modules = params.modules // remove the dot -> can be used in bash scripts
 
 //////// end Variables
@@ -43,27 +46,9 @@ ref_ch_test = file("${ref_path}/${ref_file}") // to test if exist below
 //////// Channels
 
 fastq_ch = Channel.fromPath("${in_path}/${fastq_file}", checkIfExists: false) // I could use true, but I prefer to perform the check below, in order to have a more explicit error message
-primer_ch = Channel.fromPath("${primer_fasta}", checkIfExists: false) // I could use true, but I prefer to perform the check below, in order to have a more explicit error message
-Channel.fromPath("${ref_path}/${ref_file}", checkIfExists: false).into{ref_ch1 ; ref_ch2 ; ref_ch3} // I could use true, but I prefer to perform the check below, in order to have a more explicit error message
-alien_l_param_ch = Channel.from("${alientrimmer_l_param}")
-Channel.from("${attc_seq}").into{attc_seq_ch1 ; attc_seq_ch2}
-fivep_seq_filtering_ch = Channel.from("${fivep_seq_filtering}")
-fivep_seq_nb_ch = Channel.from("${fivep_seq_nb}")
-added_nb_ch = Channel.from("${added_nb}")
-sum_ch = Channel.from("${fivep_seq_nb}", "${added_nb}").toInteger().sum()
-Channel.from("${cute_path}").into{cute_ch1 ; cute_ch2 ; cute_ch3 ; cute_ch4 ; cute_ch5 ; cute_ch6 ; cute_ch7 ; cute_ch8 ; cute_ch9}
-cutoff_nb_ch = Channel.from("${cutoff_nb}")
-Channel.from("${ori_coord}").into{ori_coord_ch1 ; ori_coord_ch2}
-Channel.from("${ter_coord}").into{ter_coord_ch1 ; ter_coord_ch2}
-Channel.from("${color_coverage}").into{color_coverage_ch1 ; color_coverage_ch2}
-Channel.from("${xlab}").into{xlab_ch1 ; xlab_ch2}
-Channel.from("${ref_name}").into{ref_name_ch1 ; ref_name_ch2}
-Channel.from("${genome_size}").into{genome_size_ch1 ; genome_size_ch2}
 
 //////// end Channels
 
-
-
 //////// Checks
 
 if(system_exec == 'local' || system_exec == 'slurm'){
@@ -91,7 +76,7 @@ if(system_exec == 'local' || system_exec == 'slurm'){
 
 process init {
     label 'bash' // see the withLabel: bash in the nextflow config file 
-    cache 'true'
+    cache 'false'
 
     output:
     file "report.rmd" into log_ch0
@@ -145,8 +130,8 @@ process trim { // Trim the oligo sequences. See section 8.4 of the labbook 20200
     input:
     val file_name
     file gz from fastq_Nremove_ch
-    file pr from primer_ch
-    val alien_l_param from alien_l_param_ch
+    file pr from primer
+    val alien_l_param from alientrimmer_l_param
 
     output:
     file "${file_name}_trim.fq" into fastq_trim_ch1, fastq_trim_ch2
@@ -189,11 +174,11 @@ process fivep_filtering { // section 8.6 to 8.13 of the labbook 20200520. Instea
     input:
     val file_name
     file fq from fastq_trim_ch2
-    val fivep_seq_filtering from fivep_seq_filtering_ch
-    val attc_seq from attc_seq_ch1
-    val fivep_seq_nb from fivep_seq_nb_ch
-    val added_nb from added_nb_ch
-    val sum_of_2_nb from sum_ch
+    val fivep_seq_filtering
+    val attc_seq
+    val fivep_seq_nb
+    val added_nb
+    val sum_of_2_nb
 
     output:
     file "${file_name}_5pAtccRm.fq" into fastq_5p_filter_ch1, fastq_5p_filter_ch2
@@ -227,8 +212,8 @@ process plot_fivep_filtering_stat { // section 8.7 to 8.11 of the labbook 202005
 
     input:
     tuple val(nouse), file(stat) from stat_fastq_5p_filter_ch1
-    val attc_seq from attc_seq_ch2
-    val cute from cute_ch1
+    val attc_seq
+    val cute from cute_path
 
     output:
     file "plot_fivep_filtering_stat.png" into fig_ch1
@@ -261,7 +246,7 @@ process plot_read_length_ini { // section 8.8 of the labbook 20200520
 
     input:
     file length from length_fastq_ini_ch
-    val cute from cute_ch2
+    val cute from cute_path
 
     output:
     file "plot_read_length_ini.png" into fig_ch2
@@ -290,7 +275,7 @@ process plot_read_length_fivep_filtering { // section 8.12 of the labbook 202005
 
     input:
     file length from length_fastq_5p_filter_ch
-    val cute from cute_ch3
+    val cute from cute_path
 
     output:
     file "plot_read_length_fivep_filtering.png" into fig_ch3
@@ -318,7 +303,7 @@ process cutoff { // section 8.16 of the labbook 20200520
     input:
     val file_name
     file fq from fastq_5p_filter_ch2
-    val nb from cutoff_nb_ch
+    val nb from cutoff_nb
 
     output:
     file "${file_name}_cutoff.fq" into cutoff_ch
@@ -340,7 +325,7 @@ process plot_read_length_cutoff { // section 8.17 of the labbook 20200520
 
     input:
     file length from length_cutoff_ch
-    val cute from cute_ch4
+    val cute from cute_path
 
     output:
     file "plot_read_length_cutoff.png" into fig_ch4
@@ -394,7 +379,7 @@ process bowtie2 { // section 24.1 of the labbook 20200707
     val file_name
     val ref_name
     file fq from cutoff_ch
-    file ref from ref_ch1
+    file ref
 
     output:
     file "${file_name}_bowtie2.bam" into bowtie2_ch1, bowtie2_ch2
@@ -503,7 +488,7 @@ process duplicate_removal { // section 24.5 of the labbook 20200707. Warning: US
     input:
     val file_name
     file bam from q20_ch2
-    file ref from ref_ch2
+    file ref
 
     output:
     file "${file_name}_q20_nodup.bam" into dup_ch1, dup_ch2
@@ -585,11 +570,11 @@ process plot_coverage { // section 24.6 of the labbook 20200707
     val file_name
     file cov from cov_ch // warning: several files
     file read_nb from bow_read_nb_ch.concat(q20_read_nb_ch, dup_read_nb_ch)
-    val ori_coord from ori_coord_ch1.first()
-    val ter_coord from ter_coord_ch1.first()
-    val color_coverage from color_coverage_ch1.first()
-    val xlab from xlab_ch1.first()
-    val cute from cute_ch5.first()
+    val ori_coord
+    val ter_coord
+    val color_coverage
+    val xlab
+    val cute from cute_path
 
     output:
     file "plot_${cov.baseName}.png" into fig_ch5 // warning: several files
@@ -661,11 +646,11 @@ process plot_insertion { // sections 24.7.2, 44.1 and 45.1 of the labbook 202005
     input:
     val file_name
     file pos from orient_ch1
-    val ori_coord from ori_coord_ch2
-    val ter_coord from ter_coord_ch2
-    val xlab from xlab_ch2
-    val genome_size from genome_size_ch1
-    val cute from cute_ch7
+    val ori_coord
+    val ter_coord
+    val xlab
+    val genome_size
+    val cute from cute_path
 
     output:
     file "*.png" into fig_ch6
@@ -755,8 +740,8 @@ process print_report { // section 8.8 of the labbook 20200520
 
     input:
     val file_name
-    val cute from cute_ch6
-    file report from log_ch1.concat(log_ch2, log_ch3, log_ch4, log_ch5, log_ch6, log_ch7, log_ch8, log_ch9, log_ch10, log_ch11, log_ch12, log_ch13, log_ch14, log_ch15, log_ch16, log_ch17, log_ch18, log_ch19).collectFile(name: 'report.rmd', sort: false)
+    val cute from cute_path
+    file report from log_ch0.concat(log_ch1,log_ch2, log_ch3, log_ch4, log_ch5, log_ch6, log_ch7, log_ch8, log_ch9, log_ch10, log_ch11, log_ch12, log_ch13, log_ch14, log_ch15, log_ch16, log_ch17, log_ch18, log_ch19).collectFile(name: 'report.rmd', sort: false)
     tuple val ("stat_tempo_name"), file ("stat_tempo") from stat_fastq_5p_filter_ch2
     file "plot_fivep_filtering_stat" from fig_ch1
     file "plot_read_length_ini" from fig_ch2.first()
@@ -772,7 +757,7 @@ process print_report { // section 8.8 of the labbook 20200520
 
     script:
     """
-    #cp tempo_report report.rmd # this is to get hard files, not symlinks
+    cp ${report} report_file.rmd # this is to get hard files, not symlinks
     mkdir figures
     mkdir files
     mkdir reports
@@ -784,7 +769,7 @@ process print_report { // section 8.8 of the labbook 20200520
     cp ${png} ./figures/ # Warning several files are copied using their initial names, i.e., the names they have in each work folders of the plot_coverage process
     cp ${png2} ./figures/ # Warning several files
     cp ${plot_read_length_cutoff} ./reports/nf_dag.png # trick to delude the knitting during the print report
-    Rscript $workflow.projectDir/bin/print_report.R "${cute}" "${report}" "print_report.txt"
+    print_report.R "${cute}" "report_file.rmd" "print_report.txt"
     """
 }