nf-core · znorgaard · May 14, 2025 · May 14, 2025
diff --git a/modules/nf-core/angsd/contamination/main.nf b/modules/nf-core/angsd/contamination/main.nf
@@ -27,7 +27,7 @@ process ANGSD_CONTAMINATION {
         -a ${icounts} \
         -h ${hapmap_file} \
         -p ${task.cpus} \
-        2> >(tee ${prefix}.txt >&2)
+        2>| >(tee ${prefix}.txt >&2)
 
 
     cat <<-END_VERSIONS > versions.yml

diff --git a/modules/nf-core/annosine/main.nf b/modules/nf-core/annosine/main.nf
@@ -32,7 +32,7 @@ process ANNOSINE {
         $mode \\
         $fasta \\
         $prefix \\
-        &> >(tee ${prefix}.log 2>&1)
+        &>| >(tee ${prefix}.log 2>&1)
 
     mv \\
         $prefix/Seed_SINE.fa \\

diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf
@@ -88,7 +88,7 @@ process BBMAP_BBSPLIT {
         $fastq_in \\
         $fastq_out \\
         $refstats_cmd \\
-        $args 2> >(tee ${prefix}.log >&2)
+        $args 2>| >(tee ${prefix}.log >&2)
 
     # Summary files will have an absolute path that will make the index
     # impossible to use in other processes- we can fix that

diff --git a/modules/nf-core/bowtie/align/main.nf b/modules/nf-core/bowtie/align/main.nf
@@ -38,7 +38,7 @@ process BOWTIE_ALIGN {
         $unaligned \\
         $args \\
         $endedness \\
-        2> >(tee ${prefix}.out >&2) \\
+        2>| >(tee ${prefix}.out >&2) \\
         | samtools view $args2 -@ $task.cpus -bS -o ${prefix}.bam -
 
     if [ -f ${prefix}.unmapped.fastq ]; then

diff --git a/modules/nf-core/bowtie2/align/main.nf b/modules/nf-core/bowtie2/align/main.nf
@@ -60,7 +60,7 @@ process BOWTIE2_ALIGN {
         --threads $task.cpus \\
         $unaligned \\
         $args \\
-        2> >(tee ${prefix}.bowtie2.log >&2) \\
+        2>| >(tee ${prefix}.bowtie2.log >&2) \\
         | samtools $samtools_command $args2 --threads $task.cpus ${reference} -o ${prefix}.${extension} -
 
     if [ -f ${prefix}.unmapped.fastq.1.gz ]; then

@@ -46,7 +46,7 @@ process DRAGMAP_ALIGN {
         ${args} \\
         --num-threads ${task.cpus} \\
         ${reads_command} \\
-        2> >(tee ${prefix}.dragmap.log >&2) \\
+        2>| >(tee ${prefix}.dragmap.log >&2) \\
         | samtools ${samtools_command} ${args2} --threads ${task.cpus} ${reference} -o ${prefix}.${extension} -
 
     cat <<-END_VERSIONS > versions.yml

diff --git a/modules/nf-core/faqcs/main.nf b/modules/nf-core/faqcs/main.nf
@@ -36,7 +36,7 @@ process FAQCS {
             --prefix ${prefix} \\
             -t $task.cpus \\
             $args \\
-            2> >(tee ${prefix}.log >&2)
+            2>| >(tee ${prefix}.log >&2)
 
 
         if [[ -f ${prefix}.unpaired.trimmed.fastq ]]; then
@@ -70,7 +70,7 @@ process FAQCS {
             --prefix ${meta.id} \\
             -t $task.cpus \\
             $args \\
-            2> >(tee ${prefix}.log >&2)
+            2>| >(tee ${prefix}.log >&2)
 
         # Unpaired
         if [[ -f ${prefix}.unpaired.trimmed.fastq ]]; then

diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf
@@ -48,7 +48,7 @@ process FASTP {
             $adapter_list \\
             $fail_fastq \\
             $args \\
-            2> >(tee ${prefix}.fastp.log >&2) \\
+            2>| >(tee ${prefix}.fastp.log >&2) \\
         | gzip -c > ${prefix}.fastp.fastq.gz
 
         cat <<-END_VERSIONS > versions.yml
@@ -69,7 +69,7 @@ process FASTP {
             $adapter_list \\
             $fail_fastq \\
             $args \\
-            2> >(tee ${prefix}.fastp.log >&2)
+            2>| >(tee ${prefix}.fastp.log >&2)
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
@@ -94,7 +94,7 @@ process FASTP {
             --thread $task.cpus \\
             --detect_adapter_for_pe \\
             $args \\
-            2> >(tee ${prefix}.fastp.log >&2)
+            2>| >(tee ${prefix}.fastp.log >&2)
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":

diff --git a/modules/nf-core/filtlong/main.nf b/modules/nf-core/filtlong/main.nf
@@ -28,7 +28,7 @@ process FILTLONG {
         $short_reads \\
         $args \\
         $longreads \\
-        2> >(tee ${prefix}.log >&2) \\
+        2>| >(tee ${prefix}.log >&2) \\
         | gzip -n > ${prefix}.fastq.gz
 
     cat <<-END_VERSIONS > versions.yml

diff --git a/modules/nf-core/gt/gff3/main.nf b/modules/nf-core/gt/gff3/main.nf
@@ -27,7 +27,7 @@ process GT_GFF3 {
         $args \\
         "$gff3" \\
         > "${prefix}.gt.gff3" \\
-        2> >(tee "${prefix}.error.log" >&2) \\
+        2>| >(tee "${prefix}.error.log" >&2) \\
         || echo "Errors from gt-gff3 printed to ${prefix}.error.log"
 
     if grep -q "gt gff3: error:" "${prefix}.error.log"; then

diff --git a/modules/nf-core/gt/gff3validator/main.nf b/modules/nf-core/gt/gff3validator/main.nf
@@ -25,7 +25,7 @@ process GT_GFF3VALIDATOR {
         gff3validator \\
         "$gff3" \\
         > "${prefix}.stdout" \\
-        2> >(tee "${prefix}.stderr" >&2) \\
+        2>| >(tee "${prefix}.stderr" >&2) \\
         || echo "Errors from gt-gff3validator printed to ${prefix}.error.log"
 
     if grep -q "input is valid GFF3" "${prefix}.stdout"; then

diff --git a/modules/nf-core/hifiasm/main.nf b/modules/nf-core/hifiasm/main.nf
@@ -67,7 +67,7 @@ process HIFIASM {
         ${ultralong} \\
         -o ${prefix} \\
         ${long_reads_sorted} \\
-        2> >( tee ${prefix}.stderr.log >&2 )
+        2>| >( tee ${prefix}.stderr.log >&2 )
 
     if [ -f ${prefix}.ec.fa ]; then
         gzip ${prefix}.ec.fa

diff --git a/modules/nf-core/irescue/main.nf b/modules/nf-core/irescue/main.nf
@@ -36,7 +36,7 @@ process IRESCUE {
         $genome_assembly \\
         --outdir $prefix \\
         --threads $task.cpus \\
-        $args 2> >(tee -a ${prefix}/irescue.log >&2)
+        $args 2>| >(tee -a ${prefix}/irescue.log >&2)
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/kallisto/quant/main.nf b/modules/nf-core/kallisto/quant/main.nf
@@ -57,7 +57,7 @@ process KALLISTO_QUANT {
             ${strandedness} \\
             ${args} \\
             -o $prefix \\
-            ${reads} 2> >(tee -a ${prefix}/kallisto_quant.log >&2)
+            ${reads} 2>| >(tee -a ${prefix}/kallisto_quant.log >&2)
 
     cp ${prefix}/kallisto_quant.log ${prefix}.log
     cp ${prefix}/run_info.json ${prefix}.run_info.json

diff --git a/modules/nf-core/ltrretriever/lai/main.nf b/modules/nf-core/ltrretriever/lai/main.nf
@@ -35,7 +35,7 @@ process LTRRETRIEVER_LAI {
         -t $task.cpus \\
         $monoploid_param \\
         $args \\
-        > >(tee "${prefix}.LAI.log") \\
+        >| >(tee "${prefix}.LAI.log") \\
         || echo "LAI failed! See ${prefix}.LAI.log"
 
     mv \\

diff --git a/modules/nf-core/ltrretriever/ltrretriever/main.nf b/modules/nf-core/ltrretriever/ltrretriever/main.nf
@@ -58,7 +58,7 @@ process LTRRETRIEVER_LTRRETRIEVER {
         $non_tgca_file \\
         -threads $task.cpus \\
         $args \\
-        &> >(tee "${prefix}.log" 2>&1) \\
+        &>| >(tee "${prefix}.log" 2>&1) \\
         || echo "Errors from LTR_retriever printed to ${prefix}.log"
 
     mv "${writable_genome}.pass.list"       "${prefix}.pass.list"       || echo ".pass.list was not produced"

diff --git a/modules/nf-core/mash/sketch/main.nf b/modules/nf-core/mash/sketch/main.nf
@@ -27,7 +27,7 @@ process MASH_SKETCH {
         $reads \\
         -p $task.cpus \\
         -o ${prefix} \\
-        2> >(tee ${prefix}.mash_stats >&2)
+        2>| >(tee ${prefix}.mash_stats >&2)
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/melon/main.nf b/modules/nf-core/melon/main.nf
@@ -33,7 +33,7 @@ process MELON {
         --threads $task.cpus \\
         $k2_db_arg \\
         $args \\
-        2> >(tee ${prefix}.log >&2)
+        2>| >(tee ${prefix}.log >&2)
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/merfin/hist/main.nf b/modules/nf-core/merfin/hist/main.nf
@@ -39,7 +39,7 @@ process MERFIN_HIST {
         $optional_lookup_table \\
         $optional_seqmers \\
         -output ${prefix}.hist \\
-        2> >( tee ${prefix}.hist.stderr.log )
+        2>| >( tee ${prefix}.hist.stderr.log )
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/motus/preplong/main.nf b/modules/nf-core/motus/preplong/main.nf
@@ -31,7 +31,7 @@ process MOTUS_PREPLONG {
         $refdb \\
         -t $task.cpus \\
         -o ${prefix}.gz \\
-        2> >(tee ${prefix}.log >&2)
+        2>| >(tee ${prefix}.log >&2)
 
     if [ "$db" == "" ]; then
         VERSION=\$(echo \$(motus -h 2>&1) | sed 's/^.*Version: //; s/References.*\$//')

diff --git a/modules/nf-core/motus/profile/main.nf b/modules/nf-core/motus/profile/main.nf
@@ -38,7 +38,7 @@ process MOTUS_PROFILE {
         -t $task.cpus \\
         -n $prefix \\
         -o ${prefix}.out \\
-        2> >(tee ${prefix}.log >&2)
+        2>| >(tee ${prefix}.log >&2)
 
     ## mOTUs version number is not available from command line.
     ## mOTUs save the version number in index database folder.

diff --git a/modules/nf-core/msisensor2/msi/main.nf b/modules/nf-core/msisensor2/msi/main.nf
@@ -42,7 +42,7 @@ process MSISENSOR2_MSI {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        msisensor2: \$(echo \$(msisensor2 2> >(grep Version) | sed 's/Version: v//g'))
+        msisensor2: \$(echo \$(msisensor2 2>| >(grep Version) | sed 's/Version: v//g'))
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/msisensor2/scan/main.nf b/modules/nf-core/msisensor2/scan/main.nf
@@ -30,7 +30,7 @@ process MSISENSOR2_SCAN {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        msisensor2: \$(echo \$(msisensor2 2> >(grep Version) | sed 's/Version: v//g'))
+        msisensor2: \$(echo \$(msisensor2 2>| >(grep Version) | sed 's/Version: v//g'))
     END_VERSIONS
     """
 
@@ -41,7 +41,7 @@ process MSISENSOR2_SCAN {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        msisensor2: \$(echo \$(msisensor2 2> >(grep Version) | sed 's/Version: v//g'))
+        msisensor2: \$(echo \$(msisensor2 2>| >(grep Version) | sed 's/Version: v//g'))
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/narfmap/align/main.nf b/modules/nf-core/narfmap/align/main.nf
@@ -39,7 +39,7 @@ process NARFMAP_ALIGN {
         $args \\
         --num-threads $task.cpus \\
         $reads_command \\
-        2> >(tee ${prefix}.narfmap.log >&2) \\
+        2>| >(tee ${prefix}.narfmap.log >&2) \\
         | samtools $samtools_command $args2 --threads $task.cpus ${reference} -o ${prefix}.${extension} -
 
     cat <<-END_VERSIONS > versions.yml

diff --git a/modules/nf-core/purgedups/calcuts/main.nf b/modules/nf-core/purgedups/calcuts/main.nf
@@ -22,7 +22,7 @@ process PURGEDUPS_CALCUTS {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    calcuts $args $stat > ${prefix}.cutoffs 2> >(tee ${prefix}.calcuts.log >&2)
+    calcuts $args $stat > ${prefix}.cutoffs 2>| >(tee ${prefix}.calcuts.log >&2)
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/purgedups/purgedups/main.nf b/modules/nf-core/purgedups/purgedups/main.nf
@@ -26,7 +26,7 @@ process PURGEDUPS_PURGEDUPS {
         $args \\
         -T $cutoff \\
         -c $basecov \\
-        $paf > ${prefix}.dups.bed 2> >(tee ${prefix}.purge_dups.log >&2)
+        $paf > ${prefix}.dups.bed 2>| >(tee ${prefix}.purge_dups.log >&2)
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/ragtag/patch/main.nf b/modules/nf-core/ragtag/patch/main.nf
@@ -8,11 +8,11 @@ process RAGTAG_PATCH {
         : 'biocontainers/ragtag:2.1.0--pyhb7b1952_0'}"
 
     input:
-    tuple val(meta), path(target, name: 'target/*') 
+    tuple val(meta), path(target, name: 'target/*')
     tuple val(meta2), path(query, name: 'query/*')
     tuple val(meta3), path(exclude)
     tuple val(meta4), path(skip)
-    
+
     output:
     tuple val(meta), path("*.patch.fasta"),         emit: patch_fasta
     tuple val(meta), path("*.patch.agp"),           emit: patch_agp
@@ -56,7 +56,7 @@ process RAGTAG_PATCH {
         ${arg_exclude} \\
         ${arg_skip} \\
         ${args} \\
-        2> >( tee ${prefix}.stderr.log >&2 ) \\
+        2>| >( tee ${prefix}.stderr.log >&2 ) \\
          | tee ${prefix}.stdout.log
 
     kill -TERM "\$tailpid"
@@ -76,7 +76,7 @@ process RAGTAG_PATCH {
     mv ${prefix}/ragtag.patch.err ${prefix}.patch.err
     # Move the assembly files from prefix folder, and add prefix
     for alignment_file in \$(ls ${prefix}/ragtag.patch.asm.*);
-        do 
+        do
             mv "\$alignment_file" "\${alignment_file/${prefix}\\//${prefix}_}"
         done
 
@@ -101,7 +101,7 @@ process RAGTAG_PATCH {
     touch ${prefix}.rename.fasta
     touch ${prefix}.ragtag.patch.asm.1
     touch ${prefix}.patch.err
-    
+
     cat <<-END_VERSIONS > versions.yml
         ragtag: \$(echo \$(ragtag.py -v | sed 's/v//'))
     END_VERSIONS

diff --git a/modules/nf-core/ragtag/scaffold/main.nf b/modules/nf-core/ragtag/scaffold/main.nf
@@ -51,7 +51,7 @@ process RAGTAG_SCAFFOLD {
         ${arg_skip} \\
         ${arg_hard_skip} \\
         ${args} \\
-        2> >( tee ${prefix}.stderr.log >&2 ) \\
+        2>| >( tee ${prefix}.stderr.log >&2 ) \\
         | tee ${prefix}.stdout.log
 
     mv ${prefix}/ragtag.scaffold.fasta ${prefix}.fasta

diff --git a/modules/nf-core/rseqc/bamstat/environment.yml b/modules/nf-core/rseqc/bamstat/environment.yml
@@ -5,4 +5,4 @@ channels:
   - bioconda
 dependencies:
   - bioconda::rseqc=5.0.3
-  - conda-forge::r-base>=3.5
+  - conda-forge::r-base=3.5
diff --git a/modules/nf-core/rseqc/inferexperiment/environment.yml b/modules/nf-core/rseqc/inferexperiment/environment.yml
@@ -5,4 +5,4 @@ channels:
   - bioconda
 dependencies:
   - bioconda::rseqc=5.0.3
-  - conda-forge::r-base>=3.5
+  - conda-forge::r-base=3.5
diff --git a/modules/nf-core/rseqc/innerdistance/environment.yml b/modules/nf-core/rseqc/innerdistance/environment.yml
@@ -5,4 +5,4 @@ channels:
   - bioconda
 dependencies:
   - bioconda::rseqc=5.0.3
-  - conda-forge::r-base>=3.5
+  - conda-forge::r-base=3.5
diff --git a/modules/nf-core/rseqc/junctionannotation/environment.yml b/modules/nf-core/rseqc/junctionannotation/environment.yml
@@ -5,4 +5,4 @@ channels:
   - bioconda
 dependencies:
   - bioconda::rseqc=5.0.3
-  - conda-forge::r-base>=3.5
+  - conda-forge::r-base=3.5
diff --git a/modules/nf-core/rseqc/junctionannotation/main.nf b/modules/nf-core/rseqc/junctionannotation/main.nf
@@ -33,7 +33,7 @@ process RSEQC_JUNCTIONANNOTATION {
         -r $bed \\
         -o $prefix \\
         $args \\
-        2> >(grep -v 'E::idx_find_and_load' | tee ${prefix}.junction_annotation.log >&2)
+        2>| >(grep -v 'E::idx_find_and_load' | tee ${prefix}.junction_annotation.log >&2)
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/rseqc/junctionsaturation/environment.yml b/modules/nf-core/rseqc/junctionsaturation/environment.yml
@@ -5,4 +5,4 @@ channels:
   - bioconda
 dependencies:
   - bioconda::rseqc=5.0.3
-  - conda-forge::r-base>=3.5
+  - conda-forge::r-base=3.5
diff --git a/modules/nf-core/rseqc/readdistribution/environment.yml b/modules/nf-core/rseqc/readdistribution/environment.yml
@@ -5,4 +5,4 @@ channels:
   - bioconda
 dependencies:
   - bioconda::rseqc=5.0.3
-  - conda-forge::r-base>=3.5
+  - conda-forge::r-base=3.5
diff --git a/modules/nf-core/rseqc/readduplication/environment.yml b/modules/nf-core/rseqc/readduplication/environment.yml
@@ -5,4 +5,4 @@ channels:
   - bioconda
 dependencies:
   - bioconda::rseqc=5.0.3
-  - conda-forge::r-base>=3.5
+  - conda-forge::r-base=3.5
diff --git a/modules/nf-core/rseqc/tin/environment.yml b/modules/nf-core/rseqc/tin/environment.yml
@@ -5,4 +5,4 @@ channels:
   - bioconda
 dependencies:
   - bioconda::rseqc=5.0.3
-  - conda-forge::r-base>=3.5
+  - conda-forge::r-base=3.5
diff --git a/modules/nf-core/seqkit/rmdup/main.nf b/modules/nf-core/seqkit/rmdup/main.nf
@@ -36,7 +36,7 @@ process SEQKIT_RMDUP {
         $args \\
         $fastx \\
         -o ${prefix}.${extension} \\
-        2> >(tee ${prefix}.log >&2)
+        2>| >(tee ${prefix}.log >&2)
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/syri/main.nf b/modules/nf-core/syri/main.nf
@@ -33,7 +33,7 @@ process SYRI {
         -F $file_type \\
         $args \\
         --prefix $prefix \\
-        2> >(tee "${prefix}.error.log" >&2) \\
+        2>| >(tee "${prefix}.error.log" >&2) \\
         || echo "Errors from syri printed to ${prefix}.error.log"
 
     [ -f "${prefix}syri.out" ] \\