From 5d138c8fa970e2db72d093be2b06fab777e182cf Mon Sep 17 00:00:00 2001
From: Gianna Pohl <gianna.pohl@tron-mainz.de>
Date: Tue, 6 Feb 2024 08:58:09 +0100
Subject: [PATCH 01/10] changed automated naming of software version files to
 avoid problems when process is called within a submodule

---
 modules/01_fastp.nf     | 12 ++++++------
 modules/02_bwa_aln.nf   | 28 ++++++++++++++--------------
 modules/02_bwa_mem.nf   | 16 ++++++++--------
 modules/02_bwa_mem_2.nf | 16 ++++++++--------
 modules/02_star.nf      | 12 ++++++------
 modules/03_index.nf     |  6 +++---
 6 files changed, 45 insertions(+), 45 deletions(-)

diff --git a/modules/01_fastp.nf b/modules/01_fastp.nf
index 7638f8c..a972813 100644
--- a/modules/01_fastp.nf
+++ b/modules/01_fastp.nf
@@ -16,7 +16,7 @@ process FASTP_PAIRED {
             file("${fastq2.baseName}.trimmed.fq.gz"), emit: trimmed_fastqs
         file("${name}.fastp_stats.json")
         file("${name}.fastp_stats.html")
-        file("software_versions.${task.process}.txt")
+        file("software_versions.FASTP_PAIRED.txt")
 
     """
     # --input_files needs to be forced, otherwise it is inherited from profile in tests
@@ -29,8 +29,8 @@ process FASTP_PAIRED {
     --html ${name}.fastp_stats.html \
     --thread ${params.cpus}
 
-    echo ${params.manifest} >> software_versions.${task.process}.txt
-    fastp --version 2>> software_versions.${task.process}.txt
+    echo ${params.manifest} >> software_versions.FASTP_PAIRED.txt
+    fastp --version 2>> software_versions.FASTP_PAIRED.txt
     """
 }
 
@@ -50,7 +50,7 @@ process FASTP_SINGLE {
         tuple val(name), file("${fastq1.baseName}.trimmed.fq.gz"), emit: trimmed_fastqs
         file("${name}.fastp_stats.json")
         file("${name}.fastp_stats.html")
-        file("software_versions.${task.process}.txt")
+        file("software_versions.FASTP_SINGLE.txt")
 
     """
     # --input_files needs to be forced, otherwise it is inherited from profile in tests
@@ -61,7 +61,7 @@ process FASTP_SINGLE {
     --html ${name}.fastp_stats.html \
     --thread ${params.cpus}
 
-    echo ${params.manifest} >> software_versions.${task.process}.txt
-    fastp --version 2>> software_versions.${task.process}.txt
+    echo ${params.manifest} >> software_versions.FASTP_SINGLE.txt
+    fastp --version 2>> software_versions.FASTP_SINGLE.txt
     """
 }
\ No newline at end of file
diff --git a/modules/02_bwa_aln.nf b/modules/02_bwa_aln.nf
index 7f9b4ad..c960ab2 100644
--- a/modules/02_bwa_aln.nf
+++ b/modules/02_bwa_aln.nf
@@ -12,13 +12,13 @@ process BWA_ALN {
 
     output:
         tuple val("${name}"), file("${fastq}"), file("${fastq.baseName}.sai"), emit: alignment_output
-        file("software_versions.${task.process}.txt")
+        file("software_versions.BWA_ALN.txt")
 
     """
     bwa aln -t ${task.cpus} ${params.reference} ${fastq} > ${fastq.baseName}.sai
 
-    echo ${params.manifest} >> software_versions.${task.process}.txt
-    echo "bwa=0.7.17"  >> software_versions.${task.process}.txt
+    echo ${params.manifest} >> software_versions.BWA_ALN.txt
+    echo "bwa=0.7.17"  >> software_versions.BWA_ALN.txt
     """
 }
 
@@ -37,14 +37,14 @@ process BWA_SAMPE {
 
     output:
       tuple val("${name}"), file("${name}.bam"), emit: bams
-      file("software_versions.${task.process}.txt")
+      file("software_versions.BWA_SAMPE.txt")
 
     """
     bwa sampe ${params.reference} ${sai1} ${sai2} ${fastq1} ${fastq2} | samtools view -uS - | samtools sort - > ${name}.bam
 
-    echo ${params.manifest} >> software_versions.${task.process}.txt
-    echo "bwa=0.7.17"  >> software_versions.${task.process}.txt
-    samtools --version >> software_versions.${task.process}.txt
+    echo ${params.manifest} >> software_versions.BWA_SAMPE.txt
+    echo "bwa=0.7.17"  >> software_versions.BWA_SAMPE.txt
+    samtools --version >> software_versions.BWA_SAMPE.txt
     """
 }
 
@@ -63,13 +63,13 @@ process BWA_SAMSE {
 
     output:
       tuple val("${name}"), file("${name}.bam"), emit: bams
-      file("software_versions.${task.process}.txt")
+      file("software_versions.BWA_SAMSE.txt")
 
     """
     bwa samse ${params.reference} ${sai} ${fastq} | samtools view -uS - | samtools sort - > ${name}.bam
 
-    echo ${params.manifest} >> software_versions.${task.process}.txt
-    echo "bwa=0.7.17"  >> software_versions.${task.process}.txt
+    echo ${params.manifest} >> software_versions.BWA_SAMSE.txt
+    echo "bwa=0.7.17"  >> software_versions.BWA_SAMSE.txt
     """
 }
 
@@ -89,15 +89,15 @@ process BWA_ALN_INCEPTION {
 
     output:
       tuple val("${name}"), file("${name}.bam"), emit: bams
-      file("software_versions.${task.process}.txt")
+      file("software_versions.BWA_ALN_INCEPTION.txt")
 
     """
     bwa sampe ${params.reference} <( bwa aln -t ${params.cpus} ${params.reference} ${fastq1} ) \
     <( bwa aln -t ${params.cpus} ${params.reference} ${fastq2} ) ${fastq1} ${fastq2} \
     | samtools view -uS - | samtools sort - > ${name}.bam
 
-    echo ${params.manifest} >> software_versions.${task.process}.txt
-    echo "bwa=0.7.17"  >> software_versions.${task.process}.txt
-    samtools --version >> software_versions.${task.process}.txt
+    echo ${params.manifest} >> software_versions.BWA_ALN_INCEPTION.txt
+    echo "bwa=0.7.17"  >> software_versions.BWA_ALN_INCEPTION.txt
+    samtools --version >> software_versions.BWA_ALN_INCEPTION.txt
     """
 }
diff --git a/modules/02_bwa_mem.nf b/modules/02_bwa_mem.nf
index 626a170..ac1b6b0 100644
--- a/modules/02_bwa_mem.nf
+++ b/modules/02_bwa_mem.nf
@@ -13,14 +13,14 @@ process BWA_MEM {
 
     output:
       tuple val("${name}"), file("${name}.bam"), emit: bams
-      file("software_versions.${task.process}.txt")
+      file("software_versions.BWA_MEM.txt")
 
     """
     bwa mem ${params.additional_args} -t ${task.cpus} ${params.reference} ${fastq1} ${fastq2} | samtools view -uS - | samtools sort - > ${name}.bam
 
-    echo ${params.manifest} >> software_versions.${task.process}.txt
-    echo "bwa=0.7.17"  >> software_versions.${task.process}.txt
-    samtools --version >> software_versions.${task.process}.txt
+    echo ${params.manifest} >> software_versions.BWA_MEM.txt
+    echo "bwa=0.7.17"  >> software_versions.BWA_MEM.txt
+    samtools --version >> software_versions.BWA_MEM.txt
     """
 }
 
@@ -39,13 +39,13 @@ process BWA_MEM_SE {
 
     output:
       tuple val("${name}"), file("${name}.bam"), emit: bams
-      file("software_versions.${task.process}.txt")
+      file("software_versions.BWA_MEM_SE.txt")
 
     """
     bwa mem ${params.additional_args} -t ${task.cpus} ${params.reference} ${fastq} | samtools view -uS - | samtools sort - > ${name}.bam
 
-    echo ${params.manifest} >> software_versions.${task.process}.txt
-    echo "bwa=0.7.17"  >> software_versions.${task.process}.txt
-    samtools --version >> software_versions.${task.process}.txt
+    echo ${params.manifest} >> software_versions.BWA_MEM_SE.txt
+    echo "bwa=0.7.17"  >> software_versions.BWA_MEM_SE.txt
+    samtools --version >> software_versions.BWA_MEM_SE.txt
     """
 }
diff --git a/modules/02_bwa_mem_2.nf b/modules/02_bwa_mem_2.nf
index 58ad725..e61f606 100755
--- a/modules/02_bwa_mem_2.nf
+++ b/modules/02_bwa_mem_2.nf
@@ -13,14 +13,14 @@ process BWA_MEM_2 {
 
     output:
       tuple val("${name}"), file("${name}.bam"), emit: bams
-      file("software_versions.${task.process}.txt")
+      file("software_versions.BWA_MEM_2.txt")
 
     """
     bwa-mem2 mem ${params.additional_args} -t ${task.cpus} ${params.reference} ${fastq1} ${fastq2} | samtools view -uS - | samtools sort - > ${name}.bam
 
-    echo ${params.manifest} >> software_versions.${task.process}.txt
-    bwa-mem2 version  >> software_versions.${task.process}.txt
-    samtools --version >> software_versions.${task.process}.txt
+    echo ${params.manifest} >> software_versions.BWA_MEM_2.txt
+    bwa-mem2 version  >> software_versions.BWA_MEM_2.txt
+    samtools --version >> software_versions.BWA_MEM_2.txt
     """
 }
 
@@ -39,13 +39,13 @@ process BWA_MEM_2_SE {
 
     output:
       tuple val("${name}"), file("${name}.bam"), emit: bams
-      file("software_versions.${task.process}.txt")
+      file("software_versions.BWA_MEM_2_SE.txt")
 
     """
     bwa-mem2 mem ${params.additional_args} -t ${task.cpus} ${params.reference} ${fastq} | samtools view -uS - | samtools sort - > ${name}.bam
 
-    echo ${params.manifest} >> software_versions.${task.process}.txt
-    bwa-mem2 version  >> software_versions.${task.process}.txt
-    samtools --version >> software_versions.${task.process}.txt
+    echo ${params.manifest} >> software_versions.BWA_MEM_2_SE.txt
+    bwa-mem2 version  >> software_versions.BWA_MEM_2_SE.txt
+    samtools --version >> software_versions.BWA_MEM_2_SE.txt
     """
 }
diff --git a/modules/02_star.nf b/modules/02_star.nf
index 66c1b95..948bb06 100644
--- a/modules/02_star.nf
+++ b/modules/02_star.nf
@@ -13,7 +13,7 @@ process STAR {
 
     output:
       tuple val("${name}"), file("${name}.bam"), emit: bams
-      file("software_versions.${task.process}.txt")
+      file("software_versions.STAR.txt")
 
     script:
     two_pass_mode_param = params.star_two_pass_mode ? "--twopassMode Basic" : ""
@@ -32,8 +32,8 @@ process STAR {
 
     mv ${name}.Aligned.sortedByCoord.out.bam ${name}.bam
 
-    echo ${params.manifest} >> software_versions.${task.process}.txt
-    STAR --version >> software_versions.${task.process}.txt
+    echo ${params.manifest} >> software_versions.STAR.txt
+    STAR --version >> software_versions.STAR.txt
     """
 }
 
@@ -51,7 +51,7 @@ process STAR_SE {
 
     output:
       tuple val("${name}"), file("${name}.bam"), emit: bams
-      file("software_versions.${task.process}.txt")
+      file("software_versions.STAR_SE.txt")
 
     script:
     two_pass_mode_param = params.star_two_pass_mode ? "--twopassMode Basic" : ""
@@ -70,7 +70,7 @@ process STAR_SE {
 
     mv ${name}.Aligned.sortedByCoord.out.bam ${name}.bam
 
-    echo ${params.manifest} >> software_versions.${task.process}.txt
-    STAR --version >> software_versions.${task.process}.txt
+    echo ${params.manifest} >> software_versions.STAR_SE.txt
+    STAR --version >> software_versions.STAR_SE.txt
     """
 }
diff --git a/modules/03_index.nf b/modules/03_index.nf
index a6fbcdf..7162aef 100644
--- a/modules/03_index.nf
+++ b/modules/03_index.nf
@@ -13,12 +13,12 @@ process INDEX_BAM {
 
     output:
       file("${name}.bam.bai")
-      file("software_versions.${task.process}.txt")
+      file("software_versions.INDEX_BAM.txt")
 
     """
     samtools index -@ ${task.cpus} ${bam}
 
-    echo ${params.manifest} >> software_versions.${task.process}.txt
-    samtools --version >> software_versions.${task.process}.txt
+    echo ${params.manifest} >> software_versions.INDEX_BAM.txt
+    samtools --version >> software_versions.INDEX_BAM.txt
     """
 }

From 00ff6abc34787fba64f69355b0cc81461a9b9cbf Mon Sep 17 00:00:00 2001
From: Gianna Pohl <gianna.pohl@tron-mainz.de>
Date: Tue, 6 Feb 2024 09:10:11 +0100
Subject: [PATCH 02/10] changed reference passing for easier submodule usage

---
 main.nf                 | 22 +++++++++++-----------
 modules/02_bwa_aln.nf   | 14 +++++++++-----
 modules/02_bwa_mem.nf   |  6 ++++--
 modules/02_bwa_mem_2.nf |  6 ++++--
 modules/02_star.nf      |  5 +++--
 5 files changed, 31 insertions(+), 22 deletions(-)

diff --git a/main.nf b/main.nf
index 41aa6bb..d9cac7e 100755
--- a/main.nf
+++ b/main.nf
@@ -78,25 +78,25 @@ workflow {
 
         // alignment
         if (params.algorithm == "aln" && !params.inception) {
-            BWA_ALN(trimmed_fastqs.map {name, fq1, fq2 -> tuple(name, fq1)})
-            BWA_ALN_2(trimmed_fastqs.map {name, fq1, fq2 -> tuple(name, fq2)})
-            BWA_SAMPE(BWA_ALN.out.alignment_output.join(BWA_ALN_2.out.alignment_output))
+            BWA_ALN(trimmed_fastqs.map {name, fq1, fq2 -> tuple(name, fq1)},params.reference)
+            BWA_ALN_2(trimmed_fastqs.map {name, fq1, fq2 -> tuple(name, fq2)},params.reference)
+            BWA_SAMPE(BWA_ALN.out.alignment_output.join(BWA_ALN_2.out.alignment_output),params.reference)
             output_bams = BWA_SAMPE.out.bams
         }
         else if (params.algorithm == "aln" && params.inception) {
-            BWA_ALN_INCEPTION(trimmed_fastqs)
+            BWA_ALN_INCEPTION(trimmed_fastqs,params.reference)
             output_bams = BWA_ALN_INCEPTION.out.bams
         }
         else if (params.algorithm == "mem") {
-            BWA_MEM(trimmed_fastqs)
+            BWA_MEM(trimmed_fastqs,params.reference)
             output_bams = BWA_MEM.out.bams
         }
         else if (params.algorithm == "mem2") {
-            BWA_MEM_2(trimmed_fastqs)
+            BWA_MEM_2(trimmed_fastqs,params.reference)
             output_bams = BWA_MEM_2.out.bams
         }
         else if (params.algorithm == "star") {
-            STAR(trimmed_fastqs)
+            STAR(trimmed_fastqs,params.reference)
             output_bams = STAR.out.bams
         }
         else {
@@ -112,20 +112,20 @@ workflow {
             trimmed_fastqs = FASTP_SINGLE.out.trimmed_fastqs
         }
         if (params.algorithm == "aln"  && !params.inception) {
-            BWA_ALN(trimmed_fastqs)
+            BWA_ALN(trimmed_fastqs,params.reference)
             BWA_SAMSE(BWA_ALN.out.alignment_output)
             output_bams = BWA_SAMSE.out.bams
         }
         else if (params.algorithm == "mem") {
-            BWA_MEM_SE(trimmed_fastqs)
+            BWA_MEM_SE(trimmed_fastqs,params.reference)
             output_bams = BWA_MEM_SE.out.bams
         }
         else if (params.algorithm == "mem2") {
-            BWA_MEM_2_SE(trimmed_fastqs)
+            BWA_MEM_2_SE(trimmed_fastqs,params.reference)
             output_bams = BWA_MEM_2_SE.out.bams
         }
         else if (params.algorithm == "star") {
-            STAR_SE(trimmed_fastqs)
+            STAR_SE(trimmed_fastqs,params.reference)
             output_bams = STAR_SE.out.bams
         }
         else {
diff --git a/modules/02_bwa_aln.nf b/modules/02_bwa_aln.nf
index c960ab2..c7381d8 100644
--- a/modules/02_bwa_aln.nf
+++ b/modules/02_bwa_aln.nf
@@ -9,13 +9,14 @@ process BWA_ALN {
 
     input:
         tuple val(name), file(fastq)
+        val(reference)
 
     output:
         tuple val("${name}"), file("${fastq}"), file("${fastq.baseName}.sai"), emit: alignment_output
         file("software_versions.BWA_ALN.txt")
 
     """
-    bwa aln -t ${task.cpus} ${params.reference} ${fastq} > ${fastq.baseName}.sai
+    bwa aln -t ${task.cpus} ${reference} ${fastq} > ${fastq.baseName}.sai
 
     echo ${params.manifest} >> software_versions.BWA_ALN.txt
     echo "bwa=0.7.17"  >> software_versions.BWA_ALN.txt
@@ -34,13 +35,14 @@ process BWA_SAMPE {
     input:
       // joins both channels by key using the first element in the tuple, the name
       tuple val(name), file(fastq1), file(sai1), file(fastq2), file(sai2)
+      val(reference)
 
     output:
       tuple val("${name}"), file("${name}.bam"), emit: bams
       file("software_versions.BWA_SAMPE.txt")
 
     """
-    bwa sampe ${params.reference} ${sai1} ${sai2} ${fastq1} ${fastq2} | samtools view -uS - | samtools sort - > ${name}.bam
+    bwa sampe ${reference} ${sai1} ${sai2} ${fastq1} ${fastq2} | samtools view -uS - | samtools sort - > ${name}.bam
 
     echo ${params.manifest} >> software_versions.BWA_SAMPE.txt
     echo "bwa=0.7.17"  >> software_versions.BWA_SAMPE.txt
@@ -60,13 +62,14 @@ process BWA_SAMSE {
     input:
       // joins both channels by key using the first element in the tuple, the name
       tuple val(name), file(fastq), file(sai)
+      val(reference)
 
     output:
       tuple val("${name}"), file("${name}.bam"), emit: bams
       file("software_versions.BWA_SAMSE.txt")
 
     """
-    bwa samse ${params.reference} ${sai} ${fastq} | samtools view -uS - | samtools sort - > ${name}.bam
+    bwa samse ${reference} ${sai} ${fastq} | samtools view -uS - | samtools sort - > ${name}.bam
 
     echo ${params.manifest} >> software_versions.BWA_SAMSE.txt
     echo "bwa=0.7.17"  >> software_versions.BWA_SAMSE.txt
@@ -86,14 +89,15 @@ process BWA_ALN_INCEPTION {
     input:
       // joins both channels by key using the first element in the tuple, the name
       tuple val(name), file(fastq1), file(fastq2)
+      val(reference)
 
     output:
       tuple val("${name}"), file("${name}.bam"), emit: bams
       file("software_versions.BWA_ALN_INCEPTION.txt")
 
     """
-    bwa sampe ${params.reference} <( bwa aln -t ${params.cpus} ${params.reference} ${fastq1} ) \
-    <( bwa aln -t ${params.cpus} ${params.reference} ${fastq2} ) ${fastq1} ${fastq2} \
+    bwa sampe ${reference} <( bwa aln -t ${params.cpus} ${reference} ${fastq1} ) \
+    <( bwa aln -t ${params.cpus} ${reference} ${fastq2} ) ${fastq1} ${fastq2} \
     | samtools view -uS - | samtools sort - > ${name}.bam
 
     echo ${params.manifest} >> software_versions.BWA_ALN_INCEPTION.txt
diff --git a/modules/02_bwa_mem.nf b/modules/02_bwa_mem.nf
index ac1b6b0..93bf7ce 100644
--- a/modules/02_bwa_mem.nf
+++ b/modules/02_bwa_mem.nf
@@ -10,13 +10,14 @@ process BWA_MEM {
 
     input:
       tuple val(name), file(fastq1), file(fastq2)
+      val(reference)
 
     output:
       tuple val("${name}"), file("${name}.bam"), emit: bams
       file("software_versions.BWA_MEM.txt")
 
     """
-    bwa mem ${params.additional_args} -t ${task.cpus} ${params.reference} ${fastq1} ${fastq2} | samtools view -uS - | samtools sort - > ${name}.bam
+    bwa mem ${params.additional_args} -t ${task.cpus} ${reference} ${fastq1} ${fastq2} | samtools view -uS - | samtools sort - > ${name}.bam
 
     echo ${params.manifest} >> software_versions.BWA_MEM.txt
     echo "bwa=0.7.17"  >> software_versions.BWA_MEM.txt
@@ -36,13 +37,14 @@ process BWA_MEM_SE {
     input:
       // joins both channels by key using the first element in the tuple, the name
       tuple val(name), file(fastq)
+      val(reference)
 
     output:
       tuple val("${name}"), file("${name}.bam"), emit: bams
       file("software_versions.BWA_MEM_SE.txt")
 
     """
-    bwa mem ${params.additional_args} -t ${task.cpus} ${params.reference} ${fastq} | samtools view -uS - | samtools sort - > ${name}.bam
+    bwa mem ${params.additional_args} -t ${task.cpus} ${reference} ${fastq} | samtools view -uS - | samtools sort - > ${name}.bam
 
     echo ${params.manifest} >> software_versions.BWA_MEM_SE.txt
     echo "bwa=0.7.17"  >> software_versions.BWA_MEM_SE.txt
diff --git a/modules/02_bwa_mem_2.nf b/modules/02_bwa_mem_2.nf
index e61f606..03a5034 100755
--- a/modules/02_bwa_mem_2.nf
+++ b/modules/02_bwa_mem_2.nf
@@ -10,13 +10,14 @@ process BWA_MEM_2 {
 
     input:
       tuple val(name), file(fastq1), file(fastq2)
+      val(reference)
 
     output:
       tuple val("${name}"), file("${name}.bam"), emit: bams
       file("software_versions.BWA_MEM_2.txt")
 
     """
-    bwa-mem2 mem ${params.additional_args} -t ${task.cpus} ${params.reference} ${fastq1} ${fastq2} | samtools view -uS - | samtools sort - > ${name}.bam
+    bwa-mem2 mem ${params.additional_args} -t ${task.cpus} ${reference} ${fastq1} ${fastq2} | samtools view -uS - | samtools sort - > ${name}.bam
 
     echo ${params.manifest} >> software_versions.BWA_MEM_2.txt
     bwa-mem2 version  >> software_versions.BWA_MEM_2.txt
@@ -36,13 +37,14 @@ process BWA_MEM_2_SE {
     input:
       // joins both channels by key using the first element in the tuple, the name
       tuple val(name), file(fastq)
+      val(reference)
 
     output:
       tuple val("${name}"), file("${name}.bam"), emit: bams
       file("software_versions.BWA_MEM_2_SE.txt")
 
     """
-    bwa-mem2 mem ${params.additional_args} -t ${task.cpus} ${params.reference} ${fastq} | samtools view -uS - | samtools sort - > ${name}.bam
+    bwa-mem2 mem ${params.additional_args} -t ${task.cpus} ${reference} ${fastq} | samtools view -uS - | samtools sort - > ${name}.bam
 
     echo ${params.manifest} >> software_versions.BWA_MEM_2_SE.txt
     bwa-mem2 version  >> software_versions.BWA_MEM_2_SE.txt
diff --git a/modules/02_star.nf b/modules/02_star.nf
index 948bb06..bd2d3e8 100644
--- a/modules/02_star.nf
+++ b/modules/02_star.nf
@@ -18,7 +18,7 @@ process STAR {
     script:
     two_pass_mode_param = params.star_two_pass_mode ? "--twopassMode Basic" : ""
     """
-    STAR --genomeDir ${params.reference} ${two_pass_mode_param} ${params.additional_args} \
+    STAR --genomeDir ${reference} ${two_pass_mode_param} ${params.additional_args} \
     --readFilesCommand "gzip -d -c -f" \
     --readFilesIn ${fastq1} ${fastq2} \
     --outSAMmode Full \
@@ -48,6 +48,7 @@ process STAR_SE {
 
     input:
       tuple val(name), file(fastq)
+      val(reference)
 
     output:
       tuple val("${name}"), file("${name}.bam"), emit: bams
@@ -56,7 +57,7 @@ process STAR_SE {
     script:
     two_pass_mode_param = params.star_two_pass_mode ? "--twopassMode Basic" : ""
     """
-    STAR --genomeDir ${params.reference} ${two_pass_mode_param} ${params.additional_args} \
+    STAR --genomeDir ${reference} ${two_pass_mode_param} ${params.additional_args} \
     --readFilesCommand "gzip -d -c -f" \
     --readFilesIn ${fastq} \
     --outSAMmode Full \

From 6daa929286446f75ac1ebdf128deb641cea88f90 Mon Sep 17 00:00:00 2001
From: Gianna Pohl <gianna.pohl@tron-mainz.de>
Date: Tue, 6 Feb 2024 09:30:25 +0100
Subject: [PATCH 03/10] Bugfix: added missing refrence parameter

---
 main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index d9cac7e..6f753b6 100755
--- a/main.nf
+++ b/main.nf
@@ -113,7 +113,7 @@ workflow {
         }
         if (params.algorithm == "aln"  && !params.inception) {
             BWA_ALN(trimmed_fastqs,params.reference)
-            BWA_SAMSE(BWA_ALN.out.alignment_output)
+            BWA_SAMSE(BWA_ALN.out.alignment_output,params.reference)
             output_bams = BWA_SAMSE.out.bams
         }
         else if (params.algorithm == "mem") {

From 848eda9061a0f81dcddd70a74159683f1cdfd56c Mon Sep 17 00:00:00 2001
From: Gianna Pohl <gianna.pohl@tron-mainz.de>
Date: Tue, 6 Feb 2024 15:23:49 +0100
Subject: [PATCH 04/10] added mising input parameter for reference

---
 modules/02_star.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/02_star.nf b/modules/02_star.nf
index bd2d3e8..f06d9b1 100644
--- a/modules/02_star.nf
+++ b/modules/02_star.nf
@@ -10,6 +10,7 @@ process STAR {
 
     input:
       tuple val(name), file(fastq1), file(fastq2)
+      val(reference)
 
     output:
       tuple val("${name}"), file("${name}.bam"), emit: bams

From 173ff843534080870064d1847f156b51ad762a2e Mon Sep 17 00:00:00 2001
From: Pablo Riesgo-Ferreiro <priesgoferreiro@gmail.com>
Date: Thu, 23 May 2024 13:30:10 +0000
Subject: [PATCH 05/10] add new conda.enable and useMamba

---
 nextflow.config | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/nextflow.config b/nextflow.config
index 0223a82..820a198 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -22,6 +22,8 @@ params.additional_args = ""
 profiles {
   conda {
     params.enable_conda = true
+    conda.enabled = true
+    conda.useMamba = true
   }
   debug { process.beforeScript = 'echo $HOSTNAME' }
   test {

From 5538ef9fba3e90d4523dfa0f28df5032e22fbea6 Mon Sep 17 00:00:00 2001
From: Pablo Riesgo-Ferreiro <priesgoferreiro@gmail.com>
Date: Thu, 23 May 2024 13:34:10 +0000
Subject: [PATCH 06/10] add CI profile

---
 nextflow.config      | 8 +++++---
 tests/run_test_1.sh  | 2 +-
 tests/run_test_10.sh | 2 +-
 tests/run_test_11.sh | 2 +-
 tests/run_test_12.sh | 2 +-
 tests/run_test_13.sh | 2 +-
 tests/run_test_2.sh  | 2 +-
 tests/run_test_3.sh  | 2 +-
 tests/run_test_4.sh  | 2 +-
 tests/run_test_5.sh  | 2 +-
 tests/run_test_6.sh  | 2 +-
 tests/run_test_7.sh  | 2 +-
 tests/run_test_8.sh  | 2 +-
 tests/run_test_9.sh  | 2 +-
 14 files changed, 18 insertions(+), 16 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 820a198..2a5e029 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -26,9 +26,7 @@ profiles {
     conda.useMamba = true
   }
   debug { process.beforeScript = 'echo $HOSTNAME' }
-  test {
-    params.input_files = "test_data/test_input_paired.txt"
-    params.reference = "$baseDir/test_data/ucsc.hg19.minimal.fasta"
+  ci {
     params.cpus = 1
     params.memory = "3g"
     timeline.enabled = false
@@ -36,6 +34,10 @@ profiles {
     trace.enabled = false
     dag.enabled = false
   }
+  test {
+    params.input_files = "test_data/test_input_paired.txt"
+    params.reference = "$baseDir/test_data/ucsc.hg19.minimal.fasta"
+  }
 }
 
 // Export this variable to prevent local Python libraries from conflicting with those in the container
diff --git a/tests/run_test_1.sh b/tests/run_test_1.sh
index 8105cef..eb110e0 100644
--- a/tests/run_test_1.sh
+++ b/tests/run_test_1.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 output_folder=output/test1
-nextflow main.nf -profile test,conda --output $output_folder
+nextflow main.nf -profile test,conda,ci --output $output_folder
 test -s $output_folder/TESTX_S1_L001.bam || { echo "Missing test 1 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.bam.bai || { echo "Missing test 1 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.fastp_stats.html || { echo "Missing test 1 output file!"; exit 1; }
diff --git a/tests/run_test_10.sh b/tests/run_test_10.sh
index fcda739..9b343a4 100644
--- a/tests/run_test_10.sh
+++ b/tests/run_test_10.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 output_folder=output/test10
-nextflow main.nf -profile test,conda --library single --algorithm mem2 --output $output_folder
+nextflow main.nf -profile test,conda,ci --library single --algorithm mem2 --output $output_folder
 test -s $output_folder/TESTX_S1_L001.bam || { echo "Missing test 3 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.bam.bai || { echo "Missing test 3 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.fastp_stats.html || { echo "Missing test 3 output file!"; exit 1; }
diff --git a/tests/run_test_11.sh b/tests/run_test_11.sh
index e176cb8..8b68dde 100644
--- a/tests/run_test_11.sh
+++ b/tests/run_test_11.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 output_folder=output/test11
-nextflow main.nf -profile test,conda --algorithm star --reference `pwd`/test_data --output $output_folder
+nextflow main.nf -profile test,conda,ci --algorithm star --reference `pwd`/test_data --output $output_folder
 test -s $output_folder/TESTX_S1_L001.bam || { echo "Missing test 4 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.bam.bai || { echo "Missing test 4 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.fastp_stats.html || { echo "Missing test 4 output file!"; exit 1; }
diff --git a/tests/run_test_12.sh b/tests/run_test_12.sh
index cca6ace..b7144ec 100644
--- a/tests/run_test_12.sh
+++ b/tests/run_test_12.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 output_folder=output/test12
-nextflow main.nf -profile test,conda --algorithm star --library single --reference `pwd`/test_data --output $output_folder
+nextflow main.nf -profile test,conda,ci --algorithm star --library single --reference `pwd`/test_data --output $output_folder
 test -s $output_folder/TESTX_S1_L001.bam || { echo "Missing test 4 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.bam.bai || { echo "Missing test 4 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.fastp_stats.html || { echo "Missing test 4 output file!"; exit 1; }
diff --git a/tests/run_test_13.sh b/tests/run_test_13.sh
index a59d46d..8e3a3c8 100644
--- a/tests/run_test_13.sh
+++ b/tests/run_test_13.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 output_folder=output/test13
-nextflow main.nf -profile test,conda --algorithm star --star_two_pass_mode --reference `pwd`/test_data --output $output_folder
+nextflow main.nf -profile test,conda,ci --algorithm star --star_two_pass_mode --reference `pwd`/test_data --output $output_folder
 test -s $output_folder/TESTX_S1_L001.bam || { echo "Missing test 4 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.bam.bai || { echo "Missing test 4 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.fastp_stats.html || { echo "Missing test 4 output file!"; exit 1; }
diff --git a/tests/run_test_2.sh b/tests/run_test_2.sh
index c525376..01086b0 100644
--- a/tests/run_test_2.sh
+++ b/tests/run_test_2.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 output_folder=output/test2
-nextflow main.nf -profile test,conda --inception --output $output_folder
+nextflow main.nf -profile test,conda,ci --inception --output $output_folder
 test -s $output_folder/TESTX_S1_L001.bam || { echo "Missing test 2 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.bam.bai || { echo "Missing test 2 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.fastp_stats.html || { echo "Missing test 2 output file!"; exit 1; }
diff --git a/tests/run_test_3.sh b/tests/run_test_3.sh
index 89bcc88..56be9c6 100644
--- a/tests/run_test_3.sh
+++ b/tests/run_test_3.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 output_folder=output/test3
-nextflow main.nf -profile test,conda --library single --output $output_folder
+nextflow main.nf -profile test,conda,ci --library single --output $output_folder
 test -s $output_folder/TESTX_S1_L001.bam || { echo "Missing test 3 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.bam.bai || { echo "Missing test 3 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.fastp_stats.html || { echo "Missing test 3 output file!"; exit 1; }
diff --git a/tests/run_test_4.sh b/tests/run_test_4.sh
index 67313e7..eafa40d 100644
--- a/tests/run_test_4.sh
+++ b/tests/run_test_4.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 output_folder=output/test4
-nextflow main.nf -profile test,conda --algorithm mem --output $output_folder
+nextflow main.nf -profile test,conda,ci --algorithm mem --output $output_folder
 test -s $output_folder/TESTX_S1_L001.bam || { echo "Missing test 4 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.bam.bai || { echo "Missing test 4 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.fastp_stats.html || { echo "Missing test 4 output file!"; exit 1; }
diff --git a/tests/run_test_5.sh b/tests/run_test_5.sh
index bceb660..2eb3680 100644
--- a/tests/run_test_5.sh
+++ b/tests/run_test_5.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 output_folder=output/test5
-nextflow main.nf -profile test,conda --algorithm mem --library single --output $output_folder
+nextflow main.nf -profile test,conda,ci --algorithm mem --library single --output $output_folder
 test -s $output_folder/TESTX_S1_L001.bam || { echo "Missing test 5 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.bam.bai || { echo "Missing test 5 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.fastp_stats.html || { echo "Missing test 5 output file!"; exit 1; }
diff --git a/tests/run_test_6.sh b/tests/run_test_6.sh
index f278fcb..245a1a6 100644
--- a/tests/run_test_6.sh
+++ b/tests/run_test_6.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 output_folder=output/test6
-nextflow main.nf -profile test,conda --output $output_folder --input_files false \
+nextflow main.nf -profile test,conda,ci --output $output_folder --input_files false \
 --input_fastq1 test_data/TESTX_S1_L001_R1_001.fastq.gz \
 --input_fastq2 test_data/TESTX_S1_L001_R2_001.fastq.gz --input_name test
 test -s $output_folder/test.bam || { echo "Missing test 6 output file!"; exit 1; }
diff --git a/tests/run_test_7.sh b/tests/run_test_7.sh
index ebcdeeb..0619a60 100644
--- a/tests/run_test_7.sh
+++ b/tests/run_test_7.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 output_folder=output/test7
-nextflow main.nf -profile test,conda --output $output_folder --input_files false \
+nextflow main.nf -profile test,conda,ci --output $output_folder --input_files false \
 --input_fastq1 test_data/TESTX_S1_L001_R1_001.fastq.gz \
 --library single --input_name test
 test -s $output_folder/test.bam || { echo "Missing test 7 output file!"; exit 1; }
diff --git a/tests/run_test_8.sh b/tests/run_test_8.sh
index 8005d8f..f40d476 100644
--- a/tests/run_test_8.sh
+++ b/tests/run_test_8.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 output_folder=output/test8
-nextflow main.nf -profile test,conda --algorithm mem --skip_trimming --output $output_folder
+nextflow main.nf -profile test,conda,ci --algorithm mem --skip_trimming --output $output_folder
 test -s $output_folder/TESTX_S1_L001.bam || { echo "Missing test 8 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.bam.bai || { echo "Missing test 8 output file!"; exit 1; }
 if [ -f $output_folder/TESTX_S1_L001.fastp_stats.html ]; then
diff --git a/tests/run_test_9.sh b/tests/run_test_9.sh
index 638f5f5..71a3cf0 100644
--- a/tests/run_test_9.sh
+++ b/tests/run_test_9.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 
 output_folder=output/test9
-nextflow main.nf -profile test,conda --algorithm mem2 --output $output_folder
+nextflow main.nf -profile test,conda,ci --algorithm mem2 --output $output_folder
 test -s $output_folder/TESTX_S1_L001.bam || { echo "Missing test 4 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.bam.bai || { echo "Missing test 4 output file!"; exit 1; }
 test -s $output_folder/TESTX_S1_L001.fastp_stats.html || { echo "Missing test 4 output file!"; exit 1; }

From e7599e9e31838acae6cd628ff0a61df2ecd5caeb Mon Sep 17 00:00:00 2001
From: Pablo Riesgo-Ferreiro <priesgoferreiro@gmail.com>
Date: Thu, 23 May 2024 13:38:47 +0000
Subject: [PATCH 07/10] introduce mamba in CI

---
 .github/workflows/automated_tests.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/automated_tests.yml b/.github/workflows/automated_tests.yml
index c253dfb..84de0d0 100644
--- a/.github/workflows/automated_tests.yml
+++ b/.github/workflows/automated_tests.yml
@@ -12,7 +12,9 @@ jobs:
       with:
         distribution: 'zulu' # See 'Supported distributions' for available options
         java-version: '11'
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: mamba-org/provision-with-micromamba@v16
+      with:
+        cache-env: true
     - name: Install dependencies
       run: |
         apt-get update && apt-get --assume-yes install wget make procps software-properties-common

From 1bac1216cf4b9786f9df7d9226199b1a09f65602 Mon Sep 17 00:00:00 2001
From: Pablo Riesgo-Ferreiro <priesgoferreiro@gmail.com>
Date: Thu, 23 May 2024 13:40:35 +0000
Subject: [PATCH 08/10] mamba on ci again

---
 .github/workflows/automated_tests.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/automated_tests.yml b/.github/workflows/automated_tests.yml
index 84de0d0..0b73c91 100644
--- a/.github/workflows/automated_tests.yml
+++ b/.github/workflows/automated_tests.yml
@@ -12,9 +12,9 @@ jobs:
       with:
         distribution: 'zulu' # See 'Supported distributions' for available options
         java-version: '11'
-    - uses: mamba-org/provision-with-micromamba@v16
+    - uses: mamba-org/setup-micromamba@v1
       with:
-        cache-env: true
+        cache-environment: true
     - name: Install dependencies
       run: |
         apt-get update && apt-get --assume-yes install wget make procps software-properties-common

From b8868fcf0eabeeffc1d936dc9396987083a1ad59 Mon Sep 17 00:00:00 2001
From: Pablo Riesgo-Ferreiro <priesgoferreiro@gmail.com>
Date: Thu, 23 May 2024 13:41:24 +0000
Subject: [PATCH 09/10] one more

---
 .github/workflows/automated_tests.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/automated_tests.yml b/.github/workflows/automated_tests.yml
index 0b73c91..e6e7150 100644
--- a/.github/workflows/automated_tests.yml
+++ b/.github/workflows/automated_tests.yml
@@ -13,8 +13,6 @@ jobs:
         distribution: 'zulu' # See 'Supported distributions' for available options
         java-version: '11'
     - uses: mamba-org/setup-micromamba@v1
-      with:
-        cache-environment: true
     - name: Install dependencies
       run: |
         apt-get update && apt-get --assume-yes install wget make procps software-properties-common

From a9e8dd67bbe6eb31f00c2380eb54518a227d429d Mon Sep 17 00:00:00 2001
From: Pablo Riesgo-Ferreiro <priesgoferreiro@gmail.com>
Date: Thu, 23 May 2024 13:46:39 +0000
Subject: [PATCH 10/10] remove explicit support for mamba

---
 nextflow.config | 1 -
 1 file changed, 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 2a5e029..d909fe8 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -23,7 +23,6 @@ profiles {
   conda {
     params.enable_conda = true
     conda.enabled = true
-    conda.useMamba = true
   }
   debug { process.beforeScript = 'echo $HOSTNAME' }
   ci {