Using Seqera containers for Sentieon to avoid LD_LIBRARY errors

modules/nf-core/sentieon/applyvarcal/main.nf

@@ -7,8 +7,8 @@ process SENTIEON_APPLYVARCAL {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sentieon:202308.02--h43eeafb_0' :
-        'biocontainers/sentieon:202308.02--h43eeafb_0' }"
+        'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' :
+        'nf-core/sentieon:202308.02--c641bc397cbf79d5' }"
 
     input:
     tuple val(meta), path(vcf), path(vcf_tbi), path(recal), path(recal_index), path(tranches)
@@ -24,20 +24,10 @@ process SENTIEON_APPLYVARCAL {
     task.ext.when == null || task.ext.when
 
     script:
-    // The following code sets LD_LIBRARY_PATH in the script-section when the module is run by Singularity.
-    // That turned out to be one way of overcoming the following issue with the Singularity-Sentieon-containers from galaxy, Sentieon (LD_LIBRARY_PATH) and the way Nextflow runs Singularity-containers.
-    // The galaxy container uses a runscript which is responsible for setting LD_PRELOAD properly. Nextflow executes singularity containers using `singularity exec`, which avoids the run script, leading to the LD_LIBRARY_PATH/libstdc++.so.6 error.
-    if (workflow.containerEngine in ['singularity','apptainer']) {
-        fix_ld_library_path = 'LD_LIBRARY_PATH=/usr/local/lib/:\$LD_LIBRARY_PATH;export LD_LIBRARY_PATH'
-    } else {
-        fix_ld_library_path = ''
-    }
-
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def sentieon_auth_mech_base64 = task.ext.sentieon_auth_mech_base64 ?: ''
     def sentieon_auth_data_base64 = task.ext.sentieon_auth_data_base64 ?: ''
-
     """
     if [ "\${#SENTIEON_LICENSE_BASE64}" -lt "1500" ]; then  # If the string SENTIEON_LICENSE_BASE64 is short, then it is an encrypted url.
         export SENTIEON_LICENSE=\$(echo -e "\$SENTIEON_LICENSE_BASE64" | base64 -d)
@@ -55,8 +45,6 @@ process SENTIEON_APPLYVARCAL {
         echo "Decoded and exported Sentieon test-license system environment variables"
     fi
 
-    $fix_ld_library_path
-
     sentieon driver -r ${fasta}  --algo ApplyVarCal \\
         -v $vcf \\
         --recal $recal \\
@@ -71,19 +59,8 @@ process SENTIEON_APPLYVARCAL {
     """
 
     stub:
-    // The following code sets LD_LIBRARY_PATH in the script-section when the module is run by Singularity.
-    // That turned out to be one way of overcoming the following issue with the Singularity-Sentieon-containers from galaxy, Sentieon (LD_LIBRARY_PATH) and the way Nextflow runs Singularity-containers.
-    // The galaxy container uses a runscript which is responsible for setting LD_PRELOAD properly. Nextflow executes singularity containers using `singularity exec`, which avoids the run script, leading to the LD_LIBRARY_PATH/libstdc++.so.6 error.
-    if (workflow.containerEngine in ['singularity','apptainer']) {
-        fix_ld_library_path = 'LD_LIBRARY_PATH=/usr/local/lib/:\$LD_LIBRARY_PATH;export LD_LIBRARY_PATH'
-    } else {
-        fix_ld_library_path = ''
-    }
-
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    $fix_ld_library_path
-
     touch ${prefix}.vcf.gz
     touch ${prefix}.vcf.gz.tbi
 

modules/nf-core/sentieon/bwaindex/main.nf

@@ -5,8 +5,8 @@ process SENTIEON_BWAINDEX {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sentieon:202308.02--h43eeafb_0' :
-        'biocontainers/sentieon:202308.02--h43eeafb_0' }"
+        'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' :
+        'nf-core/sentieon:202308.02--c641bc397cbf79d5' }"
 
     input:
     tuple val(meta), path(fasta)
@@ -19,20 +19,9 @@ process SENTIEON_BWAINDEX {
     task.ext.when == null || task.ext.when
 
     script:
-    // The following code sets LD_LIBRARY_PATH in the script-section when the module is run by Singularity.
-    // That turned out to be one way of overcoming the following issue with the Singularity-Sentieon-containers from galaxy, Sentieon (LD_LIBRARY_PATH) and the way Nextflow runs Singularity-containers.
-    // The galaxy container uses a runscript which is responsible for setting LD_PRELOAD properly. Nextflow executes singularity containers using `singularity exec`, which avoids the run script, leading to the LD_LIBRARY_PATH/libstdc++.so.6 error.
-    if (workflow.containerEngine in ['singularity','apptainer']) {
-        fix_ld_library_path = 'LD_LIBRARY_PATH=/usr/local/lib/:\$LD_LIBRARY_PATH;export LD_LIBRARY_PATH'
-    } else {
-        fix_ld_library_path = ''
-    }
-
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ? "bwa/${task.ext.prefix}" : "bwa/${fasta.baseName}"
     """
-    $fix_ld_library_path
-
     mkdir bwa
 
     sentieon \\
@@ -49,18 +38,7 @@ process SENTIEON_BWAINDEX {
     """
 
     stub:
-    // The following code sets LD_LIBRARY_PATH in the script-section when the module is run by Singularity.
-    // That turned out to be one way of overcoming the following issue with the Singularity-Sentieon-containers from galaxy, Sentieon (LD_LIBRARY_PATH) and the way Nextflow runs Singularity-containers.
-    // The galaxy container uses a runscript which is responsible for setting LD_PRELOAD properly. Nextflow executes singularity containers using `singularity exec`, which avoids the run script, leading to the LD_LIBRARY_PATH/libstdc++.so.6 error.
-    if (workflow.containerEngine in ['singularity','apptainer']) {
-        fix_ld_library_path = 'LD_LIBRARY_PATH=/usr/local/lib/:\$LD_LIBRARY_PATH;export LD_LIBRARY_PATH'
-    } else {
-        fix_ld_library_path = ''
-    }
-
     """
-    $fix_ld_library_path
-
     mkdir bwa
 
     touch bwa/genome.amb

modules/nf-core/sentieon/bwamem/main.nf

@@ -9,8 +9,8 @@ process SENTIEON_BWAMEM {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sentieon:202308.02--h43eeafb_0' :
-        'biocontainers/sentieon:202308.02--h43eeafb_0' }"
+        'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' :
+        'nf-core/sentieon:202308.02--c641bc397cbf79d5' }"
 
     input:
     tuple val(meta), path(reads)
@@ -26,20 +26,10 @@ process SENTIEON_BWAMEM {
     task.ext.when == null || task.ext.when
 
     script:
-    // The following code sets LD_LIBRARY_PATH in the script-section when the module is run by Singularity.
-    // That turned out to be one way of overcoming the following issue with the Singularity-Sentieon-containers from galaxy, Sentieon (LD_LIBRARY_PATH) and the way Nextflow runs Singularity-containers.
-    // The galaxy container uses a runscript which is responsible for setting LD_PRELOAD properly. Nextflow executes singularity containers using `singularity exec`, which avoids the run script, leading to the LD_LIBRARY_PATH/libstdc++.so.6 error.
-    if (workflow.containerEngine in ['singularity','apptainer']) {
-        fix_ld_library_path = 'LD_LIBRARY_PATH=/usr/local/lib/:\$LD_LIBRARY_PATH;export LD_LIBRARY_PATH'
-    } else {
-        fix_ld_library_path = ''
-    }
-
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def sentieon_auth_mech_base64 = task.ext.sentieon_auth_mech_base64 ?: ''
     def sentieon_auth_data_base64 = task.ext.sentieon_auth_data_base64 ?: ''
-
     """
     if [ "\${SENTIEON_LICSRVR_IP}" ]; then
         # NOTE: This is how pipeline users will use Sentieon in real world
@@ -59,8 +49,6 @@ process SENTIEON_BWAMEM {
         echo "If sentieon_auth_mech and sentieon_auth_data are non-empty strings, then Sentieon is mostly likely being run with some test-license."
     fi
 
-    $fix_ld_library_path
-
     INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
 
     sentieon bwa mem \\
@@ -78,19 +66,8 @@ process SENTIEON_BWAMEM {
     """
 
     stub:
-    // The following code sets LD_LIBRARY_PATH in the script-section when the module is run by Singularity.
-    // That turned out to be one way of overcoming the following issue with the Singularity-Sentieon-containers from galaxy, Sentieon (LD_LIBRARY_PATH) and the way Nextflow runs Singularity-containers.
-    // The galaxy container uses a runscript which is responsible for setting LD_PRELOAD properly. Nextflow executes singularity containers using `singularity exec`, which avoids the run script, leading to the LD_LIBRARY_PATH/libstdc++.so.6 error.
-    if (workflow.containerEngine in ['singularity','apptainer']) {
-        fix_ld_library_path = 'LD_LIBRARY_PATH=/usr/local/lib/:\$LD_LIBRARY_PATH;export LD_LIBRARY_PATH'
-    } else {
-        fix_ld_library_path = ''
-    }
-
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    $fix_ld_library_path
-
     touch ${prefix}.bam
     touch ${prefix}.bam.bai
 

modules/nf-core/sentieon/datametrics/main.nf

@@ -7,8 +7,8 @@ process SENTIEON_DATAMETRICS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sentieon:202308.02--h43eeafb_0' :
-        'biocontainers/sentieon:202308.02--h43eeafb_0' }"
+        'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' :
+        'nf-core/sentieon:202308.02--c641bc397cbf79d5' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
@@ -28,15 +28,6 @@ process SENTIEON_DATAMETRICS {
     task.ext.when == null || task.ext.when
 
     script:
-    // The following code sets LD_LIBRARY_PATH in the script-section when the module is run by Singularity.
-    // That turned out to be one way of overcoming the following issue with the Singularity-Sentieon-containers from galaxy, Sentieon (LD_LIBRARY_PATH) and the way Nextflow runs Singularity-containers.
-    // The galaxy container uses a runscript which is responsible for setting LD_PRELOAD properly. Nextflow executes singularity containers using `singularity exec`, which avoids the run script, leading to the LD_LIBRARY_PATH/libstdc++.so.6 error.
-    if (workflow.containerEngine in ['singularity','apptainer']) {
-        fix_ld_library_path = 'LD_LIBRARY_PATH=/usr/local/lib/:\$LD_LIBRARY_PATH;export LD_LIBRARY_PATH'
-    } else {
-        fix_ld_library_path = ''
-    }
-
     def args   = task.ext.args   ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def input  = bam.sort().collect{"-i $it"}.join(' ')
@@ -59,8 +50,6 @@ process SENTIEON_DATAMETRICS {
         echo "Decoded and exported Sentieon test-license system environment variables"
     fi
 
-    $fix_ld_library_path
-
     sentieon \\
         driver \\
         -t $task.cpus \\
@@ -80,19 +69,8 @@ process SENTIEON_DATAMETRICS {
     """
 
     stub:
-    // The following code sets LD_LIBRARY_PATH in the script-section when the module is run by Singularity.
-    // That turned out to be one way of overcoming the following issue with the Singularity-Sentieon-containers from galaxy, Sentieon (LD_LIBRARY_PATH) and the way Nextflow runs Singularity-containers.
-    // The galaxy container uses a runscript which is responsible for setting LD_PRELOAD properly. Nextflow executes singularity containers using `singularity exec`, which avoids the run script, leading to the LD_LIBRARY_PATH/libstdc++.so.6 error.
-    if (workflow.containerEngine in ['singularity','apptainer']) {
-        fix_ld_library_path = 'LD_LIBRARY_PATH=/usr/local/lib/:\$LD_LIBRARY_PATH;export LD_LIBRARY_PATH'
-    } else {
-        fix_ld_library_path = ''
-    }
-
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    $fix_ld_library_path
-
     touch ${prefix}_mq_metrics.txt
     touch ${prefix}_qd_metrics.txt
     touch ${prefix}_gc_summary.txt

modules/nf-core/sentieon/dedup/main.nf

@@ -7,8 +7,8 @@ process SENTIEON_DEDUP {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sentieon:202308.02--h43eeafb_0' :
-        'biocontainers/sentieon:202308.02--h43eeafb_0' }"
+        'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' :
+        'nf-core/sentieon:202308.02--c641bc397cbf79d5' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
@@ -29,15 +29,6 @@ process SENTIEON_DEDUP {
     task.ext.when == null || task.ext.when
 
     script:
-    // The following code sets LD_LIBRARY_PATH in the script-section when the module is run by Singularity.
-    // That turned out to be one way of overcoming the following issue with the Singularity-Sentieon-containers from galaxy, Sentieon (LD_LIBRARY_PATH) and the way Nextflow runs Singularity-containers.
-    // The galaxy container uses a runscript which is responsible for setting LD_PRELOAD properly. Nextflow executes singularity containers using `singularity exec`, which avoids the run script, leading to the LD_LIBRARY_PATH/libstdc++.so.6 error.
-    if (workflow.containerEngine in ['singularity','apptainer']) {
-        fix_ld_library_path = 'LD_LIBRARY_PATH=/usr/local/lib/:\$LD_LIBRARY_PATH;export LD_LIBRARY_PATH'
-    } else {
-        fix_ld_library_path = ''
-    }
-
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def args3 = task.ext.args3 ?: ''
@@ -48,7 +39,6 @@ process SENTIEON_DEDUP {
     def sentieon_auth_mech_base64 = task.ext.sentieon_auth_mech_base64 ?: ''
     def sentieon_auth_data_base64 = task.ext.sentieon_auth_data_base64 ?: ''
     def input_list = bam.collect{"-i $it"}.join(' ')
-
     """
     if [ "\${#SENTIEON_LICENSE_BASE64}" -lt "1500" ]; then  # If the string SENTIEON_LICENSE_BASE64 is short, then it is an encrypted url.
         export SENTIEON_LICENSE=\$(echo -e "\$SENTIEON_LICENSE_BASE64" | base64 -d)
@@ -66,8 +56,6 @@ process SENTIEON_DEDUP {
         echo "Decoded and exported Sentieon test-license system environment variables"
     fi
 
-    $fix_ld_library_path
-
     sentieon driver $args $input_list -r ${fasta} --algo LocusCollector $args2 --fun score_info ${prefix}.score
     sentieon driver $args3 -t $task.cpus $input_list -r ${fasta} --algo Dedup $args4 --score_info ${prefix}.score --metrics ${metrics} ${prefix}${suffix}
     # This following tsv-file is produced in order to get a proper tsv-file with Dedup-metrics for importing in MultiQC as "custom content".
@@ -81,20 +69,10 @@ process SENTIEON_DEDUP {
     """
 
     stub:
-    // The following code sets LD_LIBRARY_PATH in the script-section when the module is run by Singularity.
-    // That turned out to be one way of overcoming the following issue with the Singularity-Sentieon-containers from galaxy, Sentieon (LD_LIBRARY_PATH) and the way Nextflow runs Singularity-containers.
-    // The galaxy container uses a runscript which is responsible for setting LD_PRELOAD properly. Nextflow executes singularity containers using `singularity exec`, which avoids the run script, leading to the LD_LIBRARY_PATH/libstdc++.so.6 error.
-    if (workflow.containerEngine in ['singularity','apptainer']) {
-        fix_ld_library_path = 'LD_LIBRARY_PATH=/usr/local/lib/:\$LD_LIBRARY_PATH;export LD_LIBRARY_PATH'
-    } else {
-        fix_ld_library_path = ''
-    }
     def prefix = task.ext.prefix ?: "${meta.id}"
     def suffix = task.ext.suffix ?: ".cram"   // The suffix should be either ".cram" or ".bam".
     def metrics = task.ext.metrics ?: "${prefix}${suffix}.metrics"
     """
-    $fix_ld_library_path
-
     touch "${prefix}${suffix}"
     touch "${prefix}${suffix}\$(echo ${suffix} | sed 's/m\$/i/')"
     touch "${metrics}"

modules/nf-core/sentieon/dnamodelapply/main.nf

@@ -7,8 +7,8 @@ process SENTIEON_DNAMODELAPPLY {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sentieon:202308.02--h43eeafb_0' :
-        'biocontainers/sentieon:202308.02--h43eeafb_0' }"
+        'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' :
+        'nf-core/sentieon:202308.02--c641bc397cbf79d5' }"
 
     input:
     tuple val(meta), path(vcf), path(idx)
@@ -25,20 +25,10 @@ process SENTIEON_DNAMODELAPPLY {
     task.ext.when == null || task.ext.when
 
     script:
-    // The following code sets LD_LIBRARY_PATH in the script-section when the module is run by Singularity.
-    // That turned out to be one way of overcoming the following issue with the Singularity-Sentieon-containers from galaxy, Sentieon (LD_LIBRARY_PATH) and the way Nextflow runs Singularity-containers.
-    // The galaxy container uses a runscript which is responsible for setting LD_PRELOAD properly. Nextflow executes singularity containers using `singularity exec`, which avoids the run script, leading to the LD_LIBRARY_PATH/libstdc++.so.6 error.
-    if (workflow.containerEngine in ['singularity','apptainer']) {
-        fix_ld_library_path = 'LD_LIBRARY_PATH=/usr/local/lib/:\$LD_LIBRARY_PATH;export LD_LIBRARY_PATH'
-    } else {
-        fix_ld_library_path = ''
-    }
-
     def args      = task.ext.args   ?: ''
     def prefix    = task.ext.prefix ?: "${meta.id}"
     def sentieon_auth_mech_base64 = task.ext.sentieon_auth_mech_base64 ?: ''
     def sentieon_auth_data_base64 = task.ext.sentieon_auth_data_base64 ?: ''
-
     """
     if [ "\${#SENTIEON_LICENSE_BASE64}" -lt "1500" ]; then  # If the string SENTIEON_LICENSE_BASE64 is short, then it is an encrypted url.
         export SENTIEON_LICENSE=\$(echo -e "\$SENTIEON_LICENSE_BASE64" | base64 -d)
@@ -56,8 +46,6 @@ process SENTIEON_DNAMODELAPPLY {
         echo "Decoded and exported Sentieon test-license system environment variables"
     fi
 
-    $fix_ld_library_path
-
     sentieon driver \\
         -t $task.cpus \\
         -r $fasta \\
@@ -74,20 +62,8 @@ process SENTIEON_DNAMODELAPPLY {
     """
 
     stub:
-    // The following code sets LD_LIBRARY_PATH in the script-section when the module is run by Singularity.
-    // That turned out to be one way of overcoming the following issue with the Singularity-Sentieon-containers from galaxy, Sentieon (LD_LIBRARY_PATH) and the way Nextflow runs Singularity-containers.
-    // The galaxy container uses a runscript which is responsible for setting LD_PRELOAD properly. Nextflow executes singularity containers using `singularity exec`, which avoids the run script, leading to the LD_LIBRARY_PATH/libstdc++.so.6 error.
-    if (workflow.containerEngine in ['singularity','apptainer']) {
-        fix_ld_library_path = 'LD_LIBRARY_PATH=/usr/local/lib/:\$LD_LIBRARY_PATH;export LD_LIBRARY_PATH'
-    } else {
-        fix_ld_library_path = ''
-    }
-
     def prefix = task.ext.prefix ?: "${meta.id}"
-
     """
-    $fix_ld_library_path
-
     touch ${prefix}.vcf.gz
     touch ${prefix}.vcf.gz.tbi