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
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