extend logic to all main.nf

nf-core · Jul 16, 2024 · a2cd33f · a2cd33f
1 parent 76a7915
commit a2cd33f
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Showing 14 changed files with 52 additions and 249 deletions.
diff --git a/modules/nf-core/sentieon/applyvarcal/main.nf b/modules/nf-core/sentieon/applyvarcal/main.nf
@@ -3,8 +3,6 @@ process SENTIEON_APPLYVARCAL {
     label 'process_low'
     label 'sentieon'
 
-    secret 'SENTIEON_LICENSE_BASE64'
-
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' :
@@ -26,24 +24,11 @@ process SENTIEON_APPLYVARCAL {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def sentieon_auth_mech_base64 = task.ext.sentieon_auth_mech_base64 ?: ''
-    def sentieon_auth_data_base64 = task.ext.sentieon_auth_data_base64 ?: ''
+    def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64 ?
+        "export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; " :
+        ""
     """
-    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)
-    else  # Localhost license file
-        # The license file is stored as a nextflow variable like, for instance, this:
-        # nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat <sentieon_license_file.lic> | base64 -w 0)
-        export SENTIEON_LICENSE=\$(mktemp)
-        echo -e "\$SENTIEON_LICENSE_BASE64" | base64 -d > \$SENTIEON_LICENSE
-    fi
-
-    if  [ ${sentieon_auth_mech_base64} ] && [ ${sentieon_auth_data_base64} ]; then
-        # If sentieon_auth_mech_base64 and sentieon_auth_data_base64 are non-empty strings, then Sentieon is mostly likely being run with some test-license.
-        export SENTIEON_AUTH_MECH=\$(echo -n "${sentieon_auth_mech_base64}" | base64 -d)
-        export SENTIEON_AUTH_DATA=\$(echo -n "${sentieon_auth_data_base64}" | base64 -d)
-        echo "Decoded and exported Sentieon test-license system environment variables"
-    fi
+    $sentieonLicense
 
     sentieon driver -r ${fasta}  --algo ApplyVarCal \\
         -v $vcf \\

diff --git a/modules/nf-core/sentieon/bwamem/main.nf b/modules/nf-core/sentieon/bwamem/main.nf
@@ -24,7 +24,6 @@ process SENTIEON_BWAMEM {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat <sentieon_license_file.lic> | base64 -w 0)
     def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64 ?
         "export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; " :
         ""

diff --git a/modules/nf-core/sentieon/datametrics/main.nf b/modules/nf-core/sentieon/datametrics/main.nf
@@ -3,8 +3,6 @@ process SENTIEON_DATAMETRICS {
     label 'process_medium'
     label 'sentieon'
 
-    secret 'SENTIEON_LICENSE_BASE64'
-
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' :
@@ -31,24 +29,11 @@ process SENTIEON_DATAMETRICS {
     def args   = task.ext.args   ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def input  = bam.sort().collect{"-i $it"}.join(' ')
-    def sentieon_auth_mech_base64 = task.ext.sentieon_auth_mech_base64 ?: ''
-    def sentieon_auth_data_base64 = task.ext.sentieon_auth_data_base64 ?: ''
+    def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64 ?
+        "export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; " :
+        ""
     """
-    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)
-    else  # Localhost license file
-        # The license file is stored as a nextflow variable like, for instance, this:
-        # nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat <sentieon_license_file.lic> | base64 -w 0)
-        export SENTIEON_LICENSE=\$(mktemp)
-        echo -e "\$SENTIEON_LICENSE_BASE64" | base64 -d > \$SENTIEON_LICENSE
-    fi
-
-    if  [ ${sentieon_auth_mech_base64} ] && [ ${sentieon_auth_data_base64} ]; then
-        # If sentieon_auth_mech_base64 and sentieon_auth_data_base64 are non-empty strings, then Sentieon is mostly likely being run with some test-license.
-        export SENTIEON_AUTH_MECH=\$(echo -n "${sentieon_auth_mech_base64}" | base64 -d)
-        export SENTIEON_AUTH_DATA=\$(echo -n "${sentieon_auth_data_base64}" | base64 -d)
-        echo "Decoded and exported Sentieon test-license system environment variables"
-    fi
+    $sentieonLicense
 
     sentieon \\
         driver \\

diff --git a/modules/nf-core/sentieon/dedup/main.nf b/modules/nf-core/sentieon/dedup/main.nf
@@ -3,8 +3,6 @@ process SENTIEON_DEDUP {
     label 'process_medium'
     label 'sentieon'
 
-    secret 'SENTIEON_LICENSE_BASE64'
-
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' :
@@ -36,25 +34,12 @@ process SENTIEON_DEDUP {
     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"
-    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 $it"}.join(' ')
+    def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64 ?
+        "export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; " :
+        ""
     """
-    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)
-    else  # Localhost license file
-        # The license file is stored as a nextflow variable like, for instance, this:
-        # nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat <sentieon_license_file.lic> | base64 -w 0)
-        export SENTIEON_LICENSE=\$(mktemp)
-        echo -e "\$SENTIEON_LICENSE_BASE64" | base64 -d > \$SENTIEON_LICENSE
-    fi
-
-    if  [ ${sentieon_auth_mech_base64} ] && [ ${sentieon_auth_data_base64} ]; then
-        # If sentieon_auth_mech_base64 and sentieon_auth_data_base64 are non-empty strings, then Sentieon is mostly likely being run with some test-license.
-        export SENTIEON_AUTH_MECH=\$(echo -n "${sentieon_auth_mech_base64}" | base64 -d)
-        export SENTIEON_AUTH_DATA=\$(echo -n "${sentieon_auth_data_base64}" | base64 -d)
-        echo "Decoded and exported Sentieon test-license system environment variables"
-    fi
+    $sentieonLicense
 
     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}

diff --git a/modules/nf-core/sentieon/dnamodelapply/main.nf b/modules/nf-core/sentieon/dnamodelapply/main.nf
@@ -3,8 +3,6 @@ process SENTIEON_DNAMODELAPPLY {
     label 'process_high'
     label 'sentieon'
 
-    secret 'SENTIEON_LICENSE_BASE64'
-
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' :
@@ -27,24 +25,11 @@ process SENTIEON_DNAMODELAPPLY {
     script:
     def args      = task.ext.args   ?: ''
     def prefix    = task.ext.prefix ?: "${meta.id}"
-    def sentieon_auth_mech_base64 = task.ext.sentieon_auth_mech_base64 ?: ''
-    def sentieon_auth_data_base64 = task.ext.sentieon_auth_data_base64 ?: ''
+    def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64 ?
+        "export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; " :
+        ""
     """
-    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)
-    else  # Localhost license file
-        # The license file is stored as a nextflow variable like, for instance, this:
-        # nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat <sentieon_license_file.lic> | base64 -w 0)
-        export SENTIEON_LICENSE=\$(mktemp)
-        echo -e "\$SENTIEON_LICENSE_BASE64" | base64 -d > \$SENTIEON_LICENSE
-    fi
-
-    if  [ ${sentieon_auth_mech_base64} ] && [ ${sentieon_auth_data_base64} ]; then
-        # If sentieon_auth_mech_base64 and sentieon_auth_data_base64 are non-empty strings, then Sentieon is mostly likely being run with some test-license.
-        export SENTIEON_AUTH_MECH=\$(echo -n "${sentieon_auth_mech_base64}" | base64 -d)
-        export SENTIEON_AUTH_DATA=\$(echo -n "${sentieon_auth_data_base64}" | base64 -d)
-        echo "Decoded and exported Sentieon test-license system environment variables"
-    fi
+    $sentieonLicense
 
     sentieon driver \\
         -t $task.cpus \\

diff --git a/modules/nf-core/sentieon/dnascope/main.nf b/modules/nf-core/sentieon/dnascope/main.nf
@@ -3,8 +3,6 @@ process SENTIEON_DNASCOPE {
     label 'process_high'
     label 'sentieon'
 
-    secret 'SENTIEON_LICENSE_BASE64'
-
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' :
@@ -40,8 +38,6 @@ process SENTIEON_DNASCOPE {
     def model_cmd                 = ml_model                           ? " --model ${ml_model}"                  : ''
     def pcr_indel_model_cmd       = pcr_indel_model                    ? " --pcr_indel_model ${pcr_indel_model}" : ''
     def prefix                    = task.ext.prefix                    ?: "${meta.id}"
-    def sentieon_auth_mech_base64 = task.ext.sentieon_auth_mech_base64 ?: ''
-    def sentieon_auth_data_base64 = task.ext.sentieon_auth_data_base64 ?: ''
     def vcf_cmd                   = ""
     def gvcf_cmd                  = ""
     def base_cmd                  = '--algo DNAscope ' + dbsnp_cmd + ' '
@@ -54,22 +50,11 @@ process SENTIEON_DNASCOPE {
         gvcf_cmd = base_cmd + args3 + ' ' + model_cmd + pcr_indel_model_cmd + ' --emit_mode gvcf ' + prefix + '.g.vcf.gz'
     }
 
+    def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64 ?
+        "export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; " :
+        ""
     """
-    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)
-    else  # Localhost license file
-        # The license file is stored as a nextflow variable like, for instance, this:
-        # nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat <sentieon_license_file.lic> | base64 -w 0)
-        export SENTIEON_LICENSE=\$(mktemp)
-        echo -e "\$SENTIEON_LICENSE_BASE64" | base64 -d > \$SENTIEON_LICENSE
-    fi
-
-    if  [ ${sentieon_auth_mech_base64} ] && [ ${sentieon_auth_data_base64} ]; then
-        # If sentieon_auth_mech_base64 and sentieon_auth_data_base64 are non-empty strings, then Sentieon is mostly likely being run with some test-license.
-        export SENTIEON_AUTH_MECH=\$(echo -n "${sentieon_auth_mech_base64}" | base64 -d)
-        export SENTIEON_AUTH_DATA=\$(echo -n "${sentieon_auth_data_base64}" | base64 -d)
-        echo "Decoded and exported Sentieon test-license system environment variables"
-    fi
+    $sentieonLicense
 
     sentieon driver $args -r $fasta -t $task.cpus -i $bam $interval $vcf_cmd $gvcf_cmd
 

diff --git a/modules/nf-core/sentieon/gvcftyper/main.nf b/modules/nf-core/sentieon/gvcftyper/main.nf
@@ -27,26 +27,13 @@ process SENTIEON_GVCFTYPER {
 
     script:
     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 ?: ''
     def gvcfs_input = '-v ' + gvcfs.join(' -v ')
     def dbsnp_cmd = dbsnp ? "--dbsnp $dbsnp" : ""
+    def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64 ?
+        "export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; " :
+        ""
     """
-    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)
-    else  # Localhost license file
-        # The license file is stored as a nextflow variable like, for instance, this:
-        # nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat <sentieon_license_file.lic> | base64 -w 0)
-        export SENTIEON_LICENSE=\$(mktemp)
-        echo -e "\$SENTIEON_LICENSE_BASE64" | base64 -d > \$SENTIEON_LICENSE
-    fi
-
-    if  [ ${sentieon_auth_mech_base64} ] && [ ${sentieon_auth_data_base64} ]; then
-        # If sentieon_auth_mech_base64 and sentieon_auth_data_base64 are non-empty strings, then Sentieon is mostly likely being run with some test-license.
-        export SENTIEON_AUTH_MECH=\$(echo -n "${sentieon_auth_mech_base64}" | base64 -d)
-        export SENTIEON_AUTH_DATA=\$(echo -n "${sentieon_auth_data_base64}" | base64 -d)
-        echo "Decoded and exported Sentieon test-license system environment variables"
-    fi
+    $sentieonLicense
 
     sentieon driver -r ${fasta} --algo GVCFtyper ${gvcfs_input} ${dbsnp_cmd} ${prefix}.vcf.gz
 

diff --git a/modules/nf-core/sentieon/haplotyper/main.nf b/modules/nf-core/sentieon/haplotyper/main.nf
@@ -3,8 +3,6 @@ process SENTIEON_HAPLOTYPER {
     label 'process_medium'
     label 'sentieon'
 
-    secret 'SENTIEON_LICENSE_BASE64'
-
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' :
@@ -36,8 +34,6 @@ process SENTIEON_HAPLOTYPER {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def dbsnp_command = dbsnp ? "-d $dbsnp " : ""
     def interval_command = intervals ? "--interval $intervals" : ""
-    def sentieon_auth_mech_base64 = task.ext.sentieon_auth_mech_base64 ?: ''
-    def sentieon_auth_data_base64 = task.ext.sentieon_auth_data_base64 ?: ''
     def vcf_cmd = ""
     def gvcf_cmd = ""
     def base_cmd = '--algo Haplotyper ' + dbsnp_command
@@ -50,22 +46,11 @@ process SENTIEON_HAPLOTYPER {
         gvcf_cmd = base_cmd + args3 + ' --emit_mode gvcf ' + prefix + '.g.vcf.gz'
     }
 
+    def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64 ?
+        "export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; " :
+        ""
     """
-    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)
-    else  # Localhost license file
-        # The license file is stored as a nextflow variable like, for instance, this:
-        # nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat <sentieon_license_file.lic> | base64 -w 0)
-        export SENTIEON_LICENSE=\$(mktemp)
-        echo -e "\$SENTIEON_LICENSE_BASE64" | base64 -d > \$SENTIEON_LICENSE
-    fi
-
-    if  [ ${sentieon_auth_mech_base64} ] && [ ${sentieon_auth_data_base64} ]; then
-        # If sentieon_auth_mech_base64 and sentieon_auth_data_base64 are non-empty strings, then Sentieon is mostly likely being run with some test-license.
-        export SENTIEON_AUTH_MECH=\$(echo -n "${sentieon_auth_mech_base64}" | base64 -d)
-        export SENTIEON_AUTH_DATA=\$(echo -n "${sentieon_auth_data_base64}" | base64 -d)
-        echo "Decoded and exported Sentieon test-license system environment variables"
-    fi
+    $sentieonLicense
 
     sentieon driver $args -r $fasta -t $task.cpus -i $input $interval_command $vcf_cmd $gvcf_cmd
 

diff --git a/modules/nf-core/sentieon/readwriter/main.nf b/modules/nf-core/sentieon/readwriter/main.nf
@@ -3,8 +3,6 @@ process SENTIEON_READWRITER {
     label 'process_medium'
     label 'sentieon'
 
-    secret 'SENTIEON_LICENSE_BASE64'
-
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' :
@@ -34,25 +32,11 @@ process SENTIEON_READWRITER {
     def prefix          = task.ext.prefix ?: "${meta.id}"
     format              = input.extension == "bam" ? "bam"     : "cram"
     index               = format          == "bam" ? "bam.bai" : "cram.crai"
-    def sentieon_auth_mech_base64 = task.ext.sentieon_auth_mech_base64 ?: ''
-    def sentieon_auth_data_base64 = task.ext.sentieon_auth_data_base64 ?: ''
+    def sentieonLicense = secrets.SENTIEON_LICENSE_BASE64 ?
+        "export SENTIEON_LICENSE=\$(mktemp);echo -e \"${secrets.SENTIEON_LICENSE_BASE64}\" | base64 -d > \$SENTIEON_LICENSE; " :
+        ""
     """
-    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)
-    else  # Localhost license file
-        # The license file is stored as a nextflow variable like, for instance, this:
-        # nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat <sentieon_license_file.lic> | base64 -w 0)
-        export SENTIEON_LICENSE=\$(mktemp)
-        echo -e "\$SENTIEON_LICENSE_BASE64" | base64 -d > \$SENTIEON_LICENSE
-    fi
-
-    if  [ ${sentieon_auth_mech_base64} ] && [ ${sentieon_auth_data_base64} ]; then
-        # If sentieon_auth_mech_base64 and sentieon_auth_data_base64 are non-empty strings, then Sentieon is mostly likely being run with some test-license.
-        export SENTIEON_AUTH_MECH=\$(echo -n "${sentieon_auth_mech_base64}" | base64 -d)
-        export SENTIEON_AUTH_DATA=\$(echo -n "${sentieon_auth_data_base64}" | base64 -d)
-        echo "Decoded and exported Sentieon test-license system environment variables"
-    fi
-
+    $sentieonLicense
 
     sentieon \\
         driver \\