Add library parameter to samplesheet (#88)

* adding library parameter to the samplesheet for normal mode and parallel mode * update test_10 samples input samplesheet * substitute params.library_name by meta.library * add default outdir [ci skip] * relabel tbfull [ci skip] * remove custom process_max label [ci skip] * add retry label [ci skip] * remove the requirement of library field from tbfull [ci skip] * use custom process label for tbfull [ci skip] * update the pipeline schema * disable the publication of renamed files [ci skip] --------- Co-authored-by: Abhinav Sharma <[email protected]> Co-authored-by: Abhinav Sharma <[email protected]>
mycobactopia-org · Aug 30, 2024 · 8b3cffc · 8b3cffc
1 parent 9b8ef94
commit 8b3cffc
Show file tree

Hide file tree

Showing 20 changed files with 189 additions and 104 deletions.
diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
@@ -1,3 +1,3 @@
-sample,fastq_1,fastq_2
-SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz
-SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,
+sample,library,fastq_1,fastq_2
+SAMPLE_PAIRED_END,illumina,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz
+SAMPLE_SINGLE_END,illumina,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz,
diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -13,6 +13,12 @@
                 "errorMessage": "Sample name must be provided and cannot contain spaces",
                 "meta": ["id"]
             },
+            "library": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "Library preparation protocol name must be provided and cannot contain spaces",
+                "meta": ["library"]
+            },
             "fastq_1": {
                 "type": "string",
                 "format": "file-path",

diff --git a/conf/base.config b/conf/base.config
@@ -51,16 +51,13 @@ process {
         memory = { check_max( 20.GB * task.attempt, 'memory'  ) }
         time   = { check_max( 16.h  * task.attempt, 'time'    ) }
     }
-    withLabel:process_max {
-        cpus = params.max_cpus
-        memory = params.max_memory
-        time = params.max_time
-    }
     withLabel:process_long {
         time   = { check_max( 20.h  * task.attempt, 'time'    ) }
     }
-    withLabel:process_high_memory {
+    withLabel:process_tbfull {
+        cpus   = 8
         memory = { check_max( 200.GB * task.attempt, 'memory' ) }
+        time   = { check_max( 336.h  * task.attempt, 'time'    ) }
     }
     withLabel:error_ignore {
         errorStrategy = 'ignore'

diff --git a/conf/modules.config b/conf/modules.config
@@ -30,6 +30,17 @@ process {
         ]
     }
 
+
+    withName: RENAME_FILES {
+        publishDir = [
+            path: { "${params.outdir}/rename_files" },
+            mode: params.publish_dir_mode,
+            enabled: false
+        ]
+    }
+
+
+
     withName: 'MULTIQC' {
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [

diff --git a/conf/test.config b/conf/test.config
@@ -24,5 +24,7 @@ params {
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
     input  = "${projectDir}/data/test_data/test_3_samples.csv"
 
+    output = "test-profile-results"
+
 
 }
diff --git a/conf/test_full.config b/conf/test_full.config
@@ -17,10 +17,9 @@ params {
     // Input data for full size test
     // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
     // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input = "${launchDir}/data/test_data/test_10_samples.csv"
+    input = "${projectDir}/data/test_data/test_10_samples.csv"
+
+    output = "test-full-profile-results"
 
-    // Fasta references
-    fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz'
 
-    input  = "${launchDir}/data/10samples.csv"
 }
diff --git a/data/test_data/publication.csv b/data/test_data/publication.csv
@@ -0,0 +1,11 @@
+sample,library,fastq_1,fastq_2
+6639-04,illumina,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552979/ERR552979_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552979/ERR552979_2.fastq.gz
+6640-04,illumina,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552647/ERR552647_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552647/ERR552647_2.fastq.gz
+6769-04,illumina,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR550/ERR550942/ERR550942_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR550/ERR550942/ERR550942_2.fastq.gz
+7520-04,illumina,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR553/ERR553024/ERR553024_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR553/ERR553024/ERR553024_2.fastq.gz
+7538-03,illumina,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552282/ERR552282_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552282/ERR552282_2.fastq.gz
+7538-03,illumina,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552281/ERR552281_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552281/ERR552281_2.fastq.gz
+8082-03,illumina,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR553/ERR553347/ERR553347_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR553/ERR553347/ERR553347_2.fastq.gz
+8864-03,illumina,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR553/ERR553000/ERR553000_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR553/ERR553000/ERR553000_2.fastq.gz
+8867-03,illumina,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR551/ERR551118/ERR551118_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR551/ERR551118/ERR551118_2.fastq.gz
+8868-03,illumina,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552427/ERR552427_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552427/ERR552427_2.fastq.gz
diff --git a/data/test_data/test_10_samples.csv b/data/test_data/test_10_samples.csv
@@ -1,12 +1,11 @@
-sample,fastq_1,fastq_2
-6639-04,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552979/ERR552979_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552979/ERR552979_2.fastq.gz
-6640-04,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552647/ERR552647_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552647/ERR552647_2.fastq.gz
-6769-04,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR550/ERR550942/ERR550942_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR550/ERR550942/ERR550942_2.fastq.gz
-7520-04,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR553/ERR553024/ERR553024_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR553/ERR553024/ERR553024_2.fastq.gz
-7538-03,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552282/ERR552282_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552282/ERR552282_2.fastq.gz
-7538-03,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552281/ERR552281_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552281/ERR552281_2.fastq.gz
-8082-03,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR553/ERR553347/ERR553347_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR553/ERR553347/ERR553347_2.fastq.gz
-8864-03,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR553/ERR553000/ERR553000_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR553/ERR553000/ERR553000_2.fastq.gz
-8867-03,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR551/ERR551118/ERR551118_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR551/ERR551118/ERR551118_2.fastq.gz
-8868-03,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552427/ERR552427_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552427/ERR552427_2.fastq.gz
-
+sample,library,fastq_1,fastq_2
+6639-04,illumina,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552979/ERR552979_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552979/ERR552979_2.fastq.gz
+6640-04,illumina,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552647/ERR552647_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552647/ERR552647_2.fastq.gz
+6769-04,illumina,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR550/ERR550942/ERR550942_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR550/ERR550942/ERR550942_2.fastq.gz
+7520-04,illumina,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR553/ERR553024/ERR553024_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR553/ERR553024/ERR553024_2.fastq.gz
+7538-03,illumina,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552282/ERR552282_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552282/ERR552282_2.fastq.gz
+7538-03,illumina,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552281/ERR552281_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552281/ERR552281_2.fastq.gz
+8082-03,illumina,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR553/ERR553347/ERR553347_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR553/ERR553347/ERR553347_2.fastq.gz
+8864-03,illumina,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR553/ERR553000/ERR553000_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR553/ERR553000/ERR553000_2.fastq.gz
+8867-03,illumina,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR551/ERR551118/ERR551118_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR551/ERR551118/ERR551118_2.fastq.gz
+8868-03,illumina,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552427/ERR552427_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552427/ERR552427_2.fastq.gz
diff --git a/data/test_data/test_3_samples.csv b/data/test_data/test_3_samples.csv
@@ -1,4 +1,4 @@
-sample,fastq_1,fastq_2
-6639-04,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552979/ERR552979_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552979/ERR552979_2.fastq.gz
-6640-04,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552647/ERR552647_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552647/ERR552647_2.fastq.gz
-6769-04,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR550/ERR550942/ERR550942_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR550/ERR550942/ERR550942_2.fastq.gz
+sample,library,fastq_1,fastq_2
+6639-04,illumina,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552979/ERR552979_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552979/ERR552979_2.fastq.gz
+6640-04,illumina,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552647/ERR552647_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR552/ERR552647/ERR552647_2.fastq.gz
+6769-04,illumina,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR550/ERR550942/ERR550942_1.fastq.gz,ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR550/ERR550942/ERR550942_2.fastq.gz
diff --git a/modules/mtbseq/tbbwa.nf b/modules/mtbseq/tbbwa.nf
@@ -6,14 +6,14 @@ process TBBWA {
     conda "bioconda::mtbseq=1.1.0"
     container "${'quay.io/biocontainers/mtbseq:1.1.0--hdfd78af_0'}"
     input:
-        tuple val(meta), path("${meta.id}_${params.library_name}_R?.fastq.gz")
+        tuple val(meta), path("${meta.id}_${meta.library}_R?.fastq.gz")
         env(USER)
         tuple path(ref_resistance_list), path(ref_interesting_regions), path(ref_gene_categories), path(ref_base_quality_recalibration)
 
     output:
-        path("Bam/${meta.id}_${params.library_name}*.{bam,bai,bamlog}")
-        tuple val(meta), path("Bam/${meta.id}_${params.library_name}*.{bam,bai}"), emit: bam_tuple
-        path("Bam/${meta.id}_${params.library_name}*.bam"), emit: bam
+        path("Bam/${meta.id}_${meta.library}*.{bam,bai,bamlog}")
+        tuple val(meta), path("Bam/${meta.id}_${meta.library}*.{bam,bai}"), emit: bam_tuple
+        path("Bam/${meta.id}_${meta.library}*.bam"), emit: bam
 
     script:
 
@@ -51,9 +51,9 @@ process TBBWA {
         touch ${task.process}_${meta.id}_err.log
 
         mkdir Bam
-        touch Bam/${meta.id}_${params.library_name}.bam
-        touch Bam/${meta.id}_${params.library_name}.bai
-        touch Bam/${meta.id}_${params.library_name}.bamlog
+        touch Bam/${meta.id}_${meta.library}.bam
+        touch Bam/${meta.id}_${meta.library}.bai
+        touch Bam/${meta.id}_${meta.library}.bamlog
 
         """
 

diff --git a/modules/mtbseq/tbfull.nf b/modules/mtbseq/tbfull.nf
@@ -1,6 +1,8 @@
 process TBFULL {
     tag "cohort"
-    label 'process_max'
+    label 'process_tbfull'
+    label 'error_retry'
+
     publishDir params.results_dir, mode: params.save_mode, enabled: params.should_publish
 
     conda "bioconda::mtbseq=1.1.0"
@@ -17,8 +19,8 @@ process TBFULL {
         path("Statistics")
         path("Statistics/Mapping_and_Variant_Statistics.tab"), emit: statistics
         path("Classification/Strain_Classification.tab"), emit: classification
-        path("Called/*_${params.library_name}*gatk_position_variants*.tab"), emit: position_variants
-        path("Position_Tables/*_${params.library_name}*.gatk_position_table.tab"), emit: position_tables
+        path("Called/*gatk_position_variants*.tab"), emit: position_variants
+        path("Position_Tables/*.gatk_position_table.tab"), emit: position_tables
         path "versions.yml", emit: versions
 
     script:
@@ -68,26 +70,25 @@ process TBFULL {
 
 
         mkdir GATK_Bam
-        touch GATK_Bam/${meta.id}_${params.library_name}.gatk.bam
-        touch GATK_Bam/${meta.id}_${params.library_name}.gatk.bai
-        touch GATK_Bam/${meta.id}_${params.library_name}.gatk.bamlog
-        touch GATK_Bam/${meta.id}_${params.library_name}.gatk.grp
-        touch GATK_Bam/${meta.id}_${params.library_name}.gatk.intervals
+        touch GATK_Bam/stub.gatk.bam
+        touch GATK_Bam/stub.gatk.bai
+        touch GATK_Bam/stub.gatk.bamlog
+        touch GATK_Bam/stub.gatk.grp
+        touch GATK_Bam/stub.gatk.intervals
         mkdir Bam
-        mkdir Bam/${meta.id}
-        touch Bam/${meta.id}_${params.library_name}.bam
-        touch Bam/${meta.id}_${params.library_name}.bai
-        touch Bam/${meta.id}_${params.library_name}.bamlog
+        touch Bam/stub.bam
+        touch Bam/stub.bai
+        touch Bam/stub.bamlog
         mkdir Called
-        touch Called/${meta.id}_${params.library_name}.gatk_position_uncovered_cf${params.mincovf}_cr${params.mincovr}_fr${params.minfreq}_ph${params.minphred}_outmode000.tab
-        touch Called/${meta.id}_${params.library_name}.gatk_position_variants_cf${params.mincovf}_cr${params.mincovr}_fr${params.minfreq}_ph${params.minphred}_outmode000.tab
+        touch Called/stub.gatk_position_uncovered_cf${params.mincovf}_cr${params.mincovr}_fr${params.minfreq}_ph${params.minphred}_outmode000.tab
+        touch Called/stub.gatk_position_variants_cf${params.mincovf}_cr${params.mincovr}_fr${params.minfreq}_ph${params.minphred}_outmode000.tab
         mkdir Mpileup
-        touch Mpileup/${meta.id}_${params.library_name}.gatk.mpileup
-        touch Mpileup/${meta.id}_${params.library_name}.gatk.mpileuplog
+        touch Mpileup/stub.gatk.mpileup
+        touch Mpileup/stub.gatk.mpileuplog
         mkdir Classification
         touch Classification/Strain_Classification.tab
         mkdir Position_Tables
-        touch Position_Tables/${meta.id}_${params.library_name}.gatk_position_table.tab
+        touch Position_Tables/stub.gatk_position_table.tab
         mkdir Statistics
         touch Statistics/Mapping_and_Variant_Statistics.tab
 

diff --git a/modules/mtbseq/tblist.nf b/modules/mtbseq/tblist.nf
@@ -6,14 +6,14 @@ process TBLIST {
     conda "bioconda::mtbseq=1.1.0"
     container "${'quay.io/biocontainers/mtbseq:1.1.0--hdfd78af_0'}"
     input:
-        tuple val(meta), path("Mpileup/${meta.id}_${params.library_name}*.gatk.mpileup")
+        tuple val(meta), path("Mpileup/${meta.id}_${meta.library}*.gatk.mpileup")
         env(USER)
         tuple path(ref_resistance_list), path(ref_interesting_regions), path(ref_gene_categories), path(ref_base_quality_recalibration)
 
     output:
-        path("Position_Tables/${meta.id}_${params.library_name}*.gatk_position_table.tab"), emit: tbjoin_input
-        tuple val(meta), path("Position_Tables/${meta.id}_${params.library_name}*.gatk_position_table.tab"), emit: position_table_tuple
-        path("Position_Tables/${meta.id}_${params.library_name}*.gatk_position_table.tab"), emit: position_table
+        path("Position_Tables/${meta.id}_${meta.library}*.gatk_position_table.tab"), emit: tbjoin_input
+        tuple val(meta), path("Position_Tables/${meta.id}_${meta.library}*.gatk_position_table.tab"), emit: position_table_tuple
+        path("Position_Tables/${meta.id}_${meta.library}*.gatk_position_table.tab"), emit: position_table
 
     script:
         def args = task.ext.args ?: "--minbqual ${params.minbqual}"
@@ -55,7 +55,7 @@ process TBLIST {
         touch ${task.process}_${meta.id}_err.log
 
         mkdir Position_Tables
-        touch Position_Tables/${meta.id}_${params.library_name}.gatk_position_table.tab
+        touch Position_Tables/${meta.id}_${meta.library}.gatk_position_table.tab
 
         """
 

diff --git a/modules/mtbseq/tbpile.nf b/modules/mtbseq/tbpile.nf
@@ -12,8 +12,8 @@ process TBPILE {
         tuple path(ref_resistance_list), path(ref_interesting_regions), path(ref_gene_categories), path(ref_base_quality_recalibration)
 
     output:
-        path("Mpileup/${meta.id}_${params.library_name}*.gatk.{mpileup,mpileuplog}")
-        tuple val(meta), path("Mpileup/${meta.id}_${params.library_name}*.gatk.mpileup"), emit: mpileup
+        path("Mpileup/${meta.id}_${meta.library}*.gatk.{mpileup,mpileuplog}")
+        tuple val(meta), path("Mpileup/${meta.id}_${meta.library}*.gatk.mpileup"), emit: mpileup
 
     script:
 
@@ -47,8 +47,8 @@ process TBPILE {
         sleep \$[ ( \$RANDOM % 10 )  + 1 ]s
 
         mkdir Mpileup
-        touch Mpileup/${meta.id}_${params.library_name}.gatk.mpileup
-        touch Mpileup/${meta.id}_${params.library_name}.gatk.mpileuplog
+        touch Mpileup/${meta.id}_${meta.library}.gatk.mpileup
+        touch Mpileup/${meta.id}_${meta.library}.gatk.mpileuplog
 
         """
 

diff --git a/modules/mtbseq/tbrefine.nf b/modules/mtbseq/tbrefine.nf
@@ -11,7 +11,7 @@ process TBREFINE {
         tuple path(ref_resistance_list), path(ref_interesting_regions), path(ref_gene_categories), path(ref_base_quality_recalibration)
 
     output:
-        tuple val(meta), path("GATK_Bam/${meta.id}_${params.library_name}*gatk.{bam,bai,bamlog,grp,intervals}"), emit: gatk_bam
+        tuple val(meta), path("GATK_Bam/${meta.id}_${meta.library}*gatk.{bam,bai,bamlog,grp,intervals}"), emit: gatk_bam
 
     script:
 
@@ -46,10 +46,10 @@ process TBREFINE {
 
 
         mkdir GATK_Bam
-        touch GATK_Bam/${meta.id}_${params.library_name}.gatk.bam
-        touch GATK_Bam/${meta.id}_${params.library_name}.gatk.bai
-        touch GATK_Bam/${meta.id}_${params.library_name}.gatk.bamlog
-        touch GATK_Bam/${meta.id}_${params.library_name}.gatk.grp
-        touch GATK_Bam/${meta.id}_${params.library_name}.gatk.intervals
+        touch GATK_Bam/${meta.id}_${meta.library}.gatk.bam
+        touch GATK_Bam/${meta.id}_${meta.library}.gatk.bai
+        touch GATK_Bam/${meta.id}_${meta.library}.gatk.bamlog
+        touch GATK_Bam/${meta.id}_${meta.library}.gatk.grp
+        touch GATK_Bam/${meta.id}_${meta.library}.gatk.intervals
         """
 }
diff --git a/modules/mtbseq/tbvariants.nf b/modules/mtbseq/tbvariants.nf
@@ -11,8 +11,8 @@ process TBVARIANTS {
         tuple path(ref_resistance_list), path(ref_interesting_regions), path(ref_gene_categories), path(ref_base_quality_recalibration)
 
     output:
-        path("Called/${meta.id}_${params.library_name}*gatk_position_{uncovered,variants}*.tab")
-        path("Called/${meta.id}_${params.library_name}*gatk_position_variants*.tab"), emit: tbjoin_input
+        path("Called/${meta.id}_${meta.library}*gatk_position_{uncovered,variants}*.tab")
+        path("Called/${meta.id}_${meta.library}*gatk_position_variants*.tab"), emit: tbjoin_input
 
     script:
         def args = task.ext.args ?: "--mincovf ${params.mincovf} --mincovr ${params.mincovr} --minphred ${params.minphred} --minfreq ${params.minfreq}"
@@ -53,8 +53,8 @@ process TBVARIANTS {
 
 
         mkdir Called
-        touch Called/${meta.id}_${params.library_name}.gatk_position_uncovered_cf${params.mincovf}_cr${params.mincovr}_fr${params.minfreq}_ph${params.minphred}_outmode000.tab
-        touch Called/${meta.id}_${params.library_name}.gatk_position_variants_cf${params.mincovf}_cr${params.mincovr}_fr${params.minfreq}_ph${params.minphred}_outmode000.tab
+        touch Called/${meta.id}_${meta.library}.gatk_position_uncovered_cf${params.mincovf}_cr${params.mincovr}_fr${params.minfreq}_ph${params.minphred}_outmode000.tab
+        touch Called/${meta.id}_${meta.library}.gatk_position_variants_cf${params.mincovf}_cr${params.mincovr}_fr${params.minfreq}_ph${params.minphred}_outmode000.tab
 
         """
 

diff --git a/modules/utils/rename_files.nf b/modules/utils/rename_files.nf
@@ -7,14 +7,14 @@ process RENAME_FILES {
         tuple val(meta), path(reads)
 
     output:
-        path("${meta.id}_${params.library_name}_R?.fastq.gz")
+        path("${meta.id}_${meta.library}_R?.fastq.gz")
 
     script:
         """
         echo "Renaming ${reads} files as per MTBseq requirements."
 
-        cp ${reads[0]} ${meta.id}_${params.library_name}_R1.fastq.gz
-        cp ${reads[1]} ${meta.id}_${params.library_name}_R2.fastq.gz
+        cp ${reads[0]} ${meta.id}_${meta.library}_R1.fastq.gz
+        cp ${reads[1]} ${meta.id}_${meta.library}_R2.fastq.gz
         """
 
 }