Fix deprecation message declarations for strict syntax compliance

modules/nf-core/bam2fastx/bam2fastq/main.nf

@@ -1,10 +1,3 @@
-def deprecation_message = """
-WARNING: This module has been deprecated. Please use nf-core/pbtk/bam2fastq
-
-Reason:
-This module is no longer fit for purpose because bam2fastx has been deprecated by PacificBiosciences
-
-"""
 process BAM2FASTX_BAM2FASTQ {
     tag "$meta.id"
     label 'process_medium'
@@ -25,9 +18,16 @@ process BAM2FASTX_BAM2FASTQ {
     task.ext.when == null || task.ext.when
 
     script:
+    def deprecation_message = """
+WARNING: This module has been deprecated. Please use nf-core/pbtk/bam2fastq
+
+Reason:
+This module is no longer fit for purpose because bam2fastx has been deprecated by PacificBiosciences
+
+"""
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    assert true: deprecation_message
+    assert false: deprecation_message
     """
     bam2fastq \\
         $args \\

modules/nf-core/bam2fastx/bam2fastq/tests/main.nf.test

@@ -27,9 +27,7 @@ nextflow_process {
 
         then {
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match()
-				}
+                { assert process.failed }
             )
         }
     }

modules/nf-core/custom/dumpsoftwareversions/main.nf

@@ -1,11 +1,3 @@
-def deprecation_message = """
-WARNING: This module has been deprecated.
-
-Reason:
-This module is no longer recommended for use, as it is replaced by the function softwareVersionsToYAML
-in the utils_nfcore_pipeline subworkflow that is included in the nf-core template.
-
-"""
 process CUSTOM_DUMPSOFTWAREVERSIONS {
     label 'process_single'
 
@@ -27,7 +19,15 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     task.ext.when == null || task.ext.when
 
     script:
-    assert true: deprecation_message
+    def deprecation_message = """
+WARNING: This module has been deprecated.
+
+Reason:
+This module is no longer recommended for use, as it is replaced by the function softwareVersionsToYAML
+in the utils_nfcore_pipeline subworkflow that is included in the nf-core template.
+
+"""
+    assert false: deprecation_message
     def args = task.ext.args ?: ''
     template 'dumpsoftwareversions.py'
 }

modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test

@@ -30,13 +30,7 @@ nextflow_process {
 
         then {
             assertAll(
-                { assert process.success },
-                { assert snapshot(
-                    process.out.versions,
-                    file(process.out.mqc_yml[0]).readLines()[0..10],
-                    file(process.out.yml[0]).readLines()[0..7]
-                    ).match()
-                }
+                { assert process.failed }
             )
         }
     }

modules/nf-core/custom/getchromsizes/main.nf

@@ -1,11 +1,3 @@
-def deprecation_message = """
-WARNING: The getchromsizes process has been deprecated. Please use nf-core/modules/samtools/faidx.
-
-Reason:
-Getting chromosome sizes was added to samtools/faidx (https://github.com/nf-core/modules/pull/7041)
-via a boolean switch, making 'getchromsizes' unnecessary.
-"""
-
 process CUSTOM_GETCHROMSIZES {
     tag "$fasta"
     label 'process_single'
@@ -28,6 +20,13 @@ process CUSTOM_GETCHROMSIZES {
     task.ext.when == null || task.ext.when
 
     script:
+    def deprecation_message = """
+WARNING: The getchromsizes process has been deprecated. Please use nf-core/modules/samtools/faidx.
+
+Reason:
+Getting chromosome sizes was added to samtools/faidx (https://github.com/nf-core/modules/pull/7041)
+via a boolean switch, making 'getchromsizes' unnecessary.
+"""
     assert false: deprecation_message
 
     def args = task.ext.args ?: ''
@@ -42,8 +41,12 @@ process CUSTOM_GETCHROMSIZES {
     """
 
     stub:
-    """
-    >&2 echo "${deprecation_message}"
-    false
-    """
+    def deprecation_message = """
+WARNING: The getchromsizes process has been deprecated. Please use nf-core/modules/samtools/faidx.
+
+Reason:
+Getting chromosome sizes was added to samtools/faidx (https://github.com/nf-core/modules/pull/7041)
+via a boolean switch, making 'getchromsizes' unnecessary.
+"""
+    assert false: deprecation_message
 }

modules/nf-core/deepvariant/main.nf

@@ -1,17 +1,3 @@
-def deprecation_message = """
-WARNING: The deepvariant process has been moved into deepvariant/rundeepvariant.
-
-Reason:
-A subworkflow "deepvariant" was added, to split DeepVariant into three processes, to help optimise
-the usage of GPU resources (https://github.com/nf-core/modules/pull/6172). The subworkflow can be
-used instead of this module. Alternatively, it is possible to use the subcommand "rundeepvariant" in
-this module. "rundeepvariant" (the process DEEPVARIANT_RUNDEEPVARIANT) is the exact same as this
-top-level process (DEEPVARIANT) used to be.
-
-The processing stages used by the subworkflow are implemented as module subcommands, e.g. makeexamples.
-"""
-
-
 process DEEPVARIANT {
     tag "$meta.id"
     label 'process_high'
@@ -36,6 +22,18 @@ process DEEPVARIANT {
     task.ext.when == null || task.ext.when
 
     script:
+    def deprecation_message = """
+WARNING: The deepvariant process has been moved into deepvariant/rundeepvariant.
+
+Reason:
+A subworkflow "deepvariant" was added, to split DeepVariant into three processes, to help optimise
+the usage of GPU resources (https://github.com/nf-core/modules/pull/6172). The subworkflow can be
+used instead of this module. Alternatively, it is possible to use the subcommand "rundeepvariant" in
+this module. "rundeepvariant" (the process DEEPVARIANT_RUNDEEPVARIANT) is the exact same as this
+top-level process (DEEPVARIANT) used to be.
+
+The processing stages used by the subworkflow are implemented as module subcommands, e.g. makeexamples.
+"""
     assert false: deprecation_message
 
 }

modules/nf-core/fcs/fcsgx/main.nf

@@ -1,10 +1,3 @@
-def deprecation_message = """
-WARNING: This module has been deprecated. Please use nf-core/modules/fcsgx/rungx
-
-Reason:
-This module is now renamed as FCSGX_RUNGX and as been updated to the latest version
-"""
-
 process FCS_FCSGX {
     tag "$meta.id"
     label 'process_low'
@@ -26,6 +19,12 @@ process FCS_FCSGX {
     task.ext.when == null || task.ext.when
 
     script:
+    def deprecation_message = """
+WARNING: This module has been deprecated. Please use nf-core/modules/fcsgx/rungx
+
+Reason:
+This module is now renamed as FCSGX_RUNGX and as been updated to the latest version
+"""
     // Comment out this block to disable the deprecation warning
     assert false: deprecation_message
 
@@ -53,6 +52,12 @@ process FCS_FCSGX {
     """
 
     stub:
+    def deprecation_message = """
+WARNING: This module has been deprecated. Please use nf-core/modules/fcsgx/rungx
+
+Reason:
+This module is now renamed as FCSGX_RUNGX and as been updated to the latest version
+"""
     // Comment out this block to disable the deprecation warning
     assert false: deprecation_message
 

modules/nf-core/kat/hist/main.nf

@@ -1,11 +1,3 @@
-def deprecation_message = """
-WARNING: This module has been deprecated. Please use nf-core/modules/merqury/merqury
-
-Reason:
-This module no longer works in conda due to glibc incompatibilities with plotting libraries
-This module is no longer maintained by the authors
-"""
-
 process KAT_HIST {
     tag "$meta.id"
     label 'process_medium'
@@ -31,6 +23,13 @@ process KAT_HIST {
     task.ext.when == null || task.ext.when
 
     script:
+    def deprecation_message = """
+WARNING: This module has been deprecated. Please use nf-core/modules/merqury/merqury
+
+Reason:
+This module no longer works in conda due to glibc incompatibilities with plotting libraries
+This module is no longer maintained by the authors
+"""
     def args   = task.ext.args   ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     assert false: deprecation_message
@@ -50,6 +49,13 @@ process KAT_HIST {
     """
 
     stub:
+    def deprecation_message = """
+WARNING: This module has been deprecated. Please use nf-core/modules/merqury/merqury
+
+Reason:
+This module no longer works in conda due to glibc incompatibilities with plotting libraries
+This module is no longer maintained by the authors
+"""
     def args      = task.ext.args   ?: ''
     def prefix    = task.ext.prefix ?: "${meta.id}"
     assert false: deprecation_message

modules/nf-core/pbbam/pbmerge/main.nf

@@ -1,10 +1,3 @@
-def deprecation_message = """
-WARNING: This module has been deprecated. Please use nf-core/pbtk/pbmerge
-
-Reason:
-This module is no longer fit for purpose because pbbam has been deprecated by PacificBiosciences
-
-"""
 process PBBAM_PBMERGE {
     tag "$meta.id"
     label 'process_low'
@@ -26,9 +19,16 @@ process PBBAM_PBMERGE {
     task.ext.when == null || task.ext.when
 
     script:
+    def deprecation_message = """
+WARNING: This module has been deprecated. Please use nf-core/pbtk/pbmerge
+
+Reason:
+This module is no longer fit for purpose because pbbam has been deprecated by PacificBiosciences
+
+"""
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    assert true: deprecation_message
+    assert false: deprecation_message
     """
     pbmerge \\
         -o ${prefix}.bam \\
@@ -42,9 +42,16 @@ process PBBAM_PBMERGE {
     """
 
     stub:
+    def deprecation_message = """
+WARNING: This module has been deprecated. Please use nf-core/pbtk/pbmerge
+
+Reason:
+This module is no longer fit for purpose because pbbam has been deprecated by PacificBiosciences
+
+"""
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    assert true: deprecation_message
+    assert false: deprecation_message
     """
     touch ${prefix}.bam
     touch ${prefix}.bam.pbi

modules/nf-core/pbbam/pbmerge/tests/main.nf.test

@@ -30,14 +30,7 @@ nextflow_process {
 
         then {
             assertAll(
-                { assert process.success },
-                { assert snapshot(
-					file(process.out.bam[0][1]).name, // With bam(), htsjdk.samtools.SAMFormatException: Error parsing SAM header. @RG line missing SM tag.
-					file(process.out.pbi[0][1]).name, //unstable
-					process.out.versions,
-                    file(process.out.versions[0]).readLines().collect { it.trim() }, // Trap to catch bioconda version mismatches
-					).match()
-				}
+                { assert process.failed }
             )
         }
     }
@@ -62,8 +55,7 @@ nextflow_process {
 
         then {
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert process.failed }
             )
         }
     }

modules/nf-core/samtools/getrg/main.nf

@@ -1,11 +1,3 @@
-def deprecation_message = """
-WARNING: This module has been deprecated. Please use nf-core/modules/samtools/splitheader
-
-Reason:
-This module has been renamed to samtools/splitheader, which has the same functionality but
-extends the outputs to include other types of SAM header.
-"""
-
 process SAMTOOLS_GETRG {
     tag "$meta.id"
     label 'process_low'
@@ -26,12 +18,26 @@ process SAMTOOLS_GETRG {
     task.ext.when == null || task.ext.when
 
     script:
+    def deprecation_message = """
+WARNING: This module has been deprecated. Please use nf-core/modules/samtools/splitheader
+
+Reason:
+This module has been renamed to samtools/splitheader, which has the same functionality but
+extends the outputs to include other types of SAM header.
+"""
     def args = task.ext.args ?: ''
     assert false: deprecation_message
     """
     """
 
     stub:
+    def deprecation_message = """
+WARNING: This module has been deprecated. Please use nf-core/modules/samtools/splitheader
+
+Reason:
+This module has been renamed to samtools/splitheader, which has the same functionality but
+extends the outputs to include other types of SAM header.
+"""
     def prefix = task.ext.prefix ?: "${meta.id}"
     assert false: deprecation_message
     """

modules/nf-core/untarfiles/main.nf

@@ -1,9 +1,3 @@
-def deprecation_message = """
-WARNING: This module has been deprecated.
-
-Reason:
-This module is no longer recommended for use. It is recommended to use nf-core/modules/untar
-"""
 process UNTARFILES {
     tag "$archive"
     label 'process_single'
@@ -24,7 +18,13 @@ process UNTARFILES {
     task.ext.when == null || task.ext.when
 
     script:
-    assert true: deprecation_message
+    def deprecation_message = """
+WARNING: This module has been deprecated.
+
+Reason:
+This module is no longer recommended for use. It is recommended to use nf-core/modules/untar
+"""
+    assert false: deprecation_message
     def args  = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     prefix    = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.baseName.toString().replaceFirst(/\.tar$/, ""))
@@ -46,7 +46,13 @@ process UNTARFILES {
     """
 
     stub:
-    assert true: deprecation_message
+    def deprecation_message = """
+WARNING: This module has been deprecated.
+
+Reason:
+This module is no longer recommended for use. It is recommended to use nf-core/modules/untar
+"""
+    assert false: deprecation_message
     prefix    = task.ext.prefix ?: "${meta.id}"
     """
     mkdir $prefix