Merge branch 'master' of gitlab.pasteur.fr:gmillot/14985_loot

bin/Nremove.sh

@@ -19,7 +19,7 @@ input_file=$1
 output_file=$2
 log=$3
 
-echo -e "<br /><br />\n\n### Removal for reads made of N only\n\n" >> ${log}
+echo -e "<br /><br />\n\n### Removal for reads made of N only\n\n" > ${log}
 zcat ${input_file} | awk '{lineKind=(NR-1)%4;}lineKind==0{record=$0; next}lineKind==1{toGet=!($0~/^N*$/); if(toGet) print record}toGet' | gzip -c > ${output_file}
 # warning: with no output dir for log.txt, the file is created in \\wsl$\Ubuntu-20.04\home\gael\work\35\b826898b7be994ff13b7bc73bc88d8\
 # get the bad sequences + 3 other lines of the fastq #see https://stackoverflow.com/questions/11793942/delete-lines-before-and-after-a-match-in-bash-with-sed-or-awk

bin/cutoff.sh

@@ -21,7 +21,7 @@ log=$4
 
 
 
-echo -e "<br /><br />\n\n### Selection of reads over ${nb} bases\n\n" >> ${log}
+echo -e "<br /><br />\n\n### Selection of reads over ${nb} bases\n\n" > ${log}
 
 # cutoff
 awk -v var1=${nb} '{lineKind=(NR-1)%4}lineKind==0{record=$0; next}lineKind==1{toGet=(length($0)>=var1); if(toGet) print record}toGet' ${input_file} > ${output_file}_cutoff.fq

bin/duplicate_removal.sh

@@ -28,7 +28,7 @@ log=$5
 # log="report.rmd"
 
 
-echo -e "<br /><br />\n\n### Removal of duplicates using the 5\' and 3\' coordinates\n\n" >> ${log}
+echo -e "<br /><br />\n\n### Removal of duplicates using the 5\' and 3\' coordinates\n\n" > ${log}
 SAMPLE_NAME=${input_file%.*} # recover the name of the file without extension
 
 # check that no BX:Z: TAG already exists

bin/fivep_filtering.sh

@@ -27,7 +27,7 @@ attc_seq=$7
 log=$8
 
 
-echo -e "<br /><br />\n\n### Selection of reads with the attC in 5'\n\n" >> ${log}
+echo -e "<br /><br />\n\n### Selection of reads with the attC in 5'\n\n" > ${log}
 # fastq filtering
 awk -v var1=${fivep_seq_filtering} '
     {lineKind=(NR-1)%4;}

bin/trim.sh

@@ -21,7 +21,7 @@ primer_fasta=$3
 alientrimmer_l_param=$4
 log=$5
 
-echo -e "<br /><br />\n\n### Trim of the read for the primer parts\n\n" >> ${log}
+echo -e "<br /><br />\n\n### Trim of the read for the primer parts\n\n" > ${log}
 # sed '/^>.*$/d' ref_seq/adapters_TruSeq_B2699.fasta > tempo.adap.seq #in case we want to remove titles of the fasta files, but no need for AlienTrimmer
 gzip ${input_file} -dc > input_file2
 AlienTrimmer -i input_file2 -c ${primer_fasta} -o ${output_file} -l ${alientrimmer_l_param} | tee tempo.txt

dev/test_slurm.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