fix: updates to sprocket CI (#226)

a-frantz · web-flow · commit 8ea01be45f0a · 2025-05-07T11:28:20.000-04:00
* fix: updates to sprocket CI

* fix: sprocket lints (other than shellcheck)

* chore: update container pulls
diff --git a/.github/workflows/sprocket-lint.yaml b/.github/workflows/sprocket-lint.yaml
@@ -14,4 +14,4 @@ jobs:
             exclude-patterns: template
             deny-warnings: true
             deny-notes: true
-            except: TrailingComma,ContainerValue
+            except: TrailingComma,ContainerUri
diff --git a/.github/workflows/validate-inputs.yaml b/.github/workflows/validate-inputs.yaml
@@ -10,6 +10,6 @@ jobs:
         - name: Validate Reference Inputs
           uses: stjude-rust-labs/sprocket-action@main
           with:
-            action: validate-inputs
+            action: validate
             wdl_files: "workflows/reference/bwa-db-build.wdl,workflows/reference/gatk-reference.wdl,workflows/reference/qc-reference.wdl,workflows/reference/star-db-build.wdl,workflows/reference/star-db-build.wdl"
             inputs_files: "workflows/reference/inputs/bwa-db-build-inputs.json,workflows/reference/inputs/gatk-reference-inputs.json,workflows/reference/inputs/qc-reference-inputs.json,workflows/reference/inputs/star-db-build-inputs.json,workflows/reference/inputs/star-db-build-mouse-contaminant-inputs.json"
diff --git a/data_structures/flag_filter.wdl b/data_structures/flag_filter.wdl
@@ -118,7 +118,7 @@ task validate_string_is_12bit_oct_dec_or_hex {
     runtime {
         memory: "4 GB"
         disks: "10 GB"
-        container: "ghcr.io/stjudecloud/util:2.1.1"
+        container: "ghcr.io/stjudecloud/util:2.1.2"
         maxRetries: 1
     }
 }
diff --git a/data_structures/read_group.wdl b/data_structures/read_group.wdl
@@ -104,7 +104,7 @@ task read_group_to_string {
     runtime {
         memory: "4 GB"
         disks: "10 GB"
-        container: "ghcr.io/stjudecloud/util:2.1.1"
+        container: "ghcr.io/stjudecloud/util:2.1.2"
         maxRetries: 1
     }
 }
@@ -441,7 +441,7 @@ task validate_read_group {
     runtime {
         memory: "4 GB"
         disks: "10 GB"
-        container: "ghcr.io/stjudecloud/util:2.1.1"
+        container: "ghcr.io/stjudecloud/util:2.1.2"
         maxRetries: 0
     }
 }
diff --git a/docker/util/package.json b/docker/util/package.json
@@ -1,4 +1,4 @@
 {
     "name": "util",
-    "version": "2.1.1"
+    "version": "2.1.2"
 }
diff --git a/tools/htseq.wdl b/tools/htseq.wdl
@@ -209,7 +209,7 @@ task calc_tpm {
     runtime {
         memory: "4 GB"
         disks: "10 GB"
-        container: "ghcr.io/stjudecloud/util:2.1.1"
+        container: "ghcr.io/stjudecloud/util:2.1.2"
         maxRetries: 1
     }
 }
diff --git a/tools/kraken2.wdl b/tools/kraken2.wdl
@@ -334,7 +334,7 @@ task kraken {
     input {
         File read_one_fastq_gz
         File read_two_fastq_gz
-        #@ except: DisallowedInputName
+        #@ except: InputName
         File db
         String prefix = sub(
             basename(read_one_fastq_gz),
diff --git a/tools/md5sum.wdl b/tools/md5sum.wdl
@@ -36,7 +36,7 @@ task compute_checksum {
     runtime {
         memory: "4 GB"
         disks: "~{disk_size_gb} GB"
-        container: "ghcr.io/stjudecloud/util:2.1.1"
+        container: "ghcr.io/stjudecloud/util:2.1.2"
         maxRetries: 1
     }
 }
diff --git a/tools/picard.wdl b/tools/picard.wdl
@@ -807,7 +807,7 @@ task quality_score_distribution {
     }
 }
 
-#@ except: NonmatchingOutput
+#@ except: MatchingOutputMeta
 task bam_to_fastq {
     meta {
         description: "**[Deprecated]** This WDL task converts the input BAM file into FASTQ format files. This task has been deprecated in favor of `samtools.bam_to_fastq` which is more performant and doesn't error on 'illegal mate states'."
diff --git a/tools/qualimap.wdl b/tools/qualimap.wdl
@@ -91,7 +91,7 @@ task rnaseq {
     }
 }
 
-#@ except: NonmatchingOutput
+#@ except: MatchingOutputMeta
 task bamqc {
     meta {
         description: "**[Deprecated]** This WDL task runs QualiMap's bamqc tool on the input BAM file. This task has been deprecated due to memory leak issues. Use at your own risk, for some samples can consume over 1TB of RAM."
diff --git a/tools/samtools.wdl b/tools/samtools.wdl
@@ -1166,7 +1166,7 @@ task position_sorted_fixmate {
     }
 }
 
-#@ except: NonmatchingOutput
+#@ except: MatchingOutputMeta
 task markdup {
     meta {
         description: "**[DEPRECATED]** Runs `samtools markdup` on the position-sorted input BAM file. This creates a report and optionally a new BAM with duplicate reads marked."
diff --git a/tools/util.wdl b/tools/util.wdl
@@ -42,7 +42,7 @@ task download {
     runtime {
         memory: "4 GB"
         disks: "~{disk_size_gb} GB"
-        container: "ghcr.io/stjudecloud/util:2.1.1"
+        container: "ghcr.io/stjudecloud/util:2.1.2"
         maxRetries: 1
     }
 }
@@ -139,7 +139,7 @@ task split_string {
     runtime {
         memory: "4 GB"
         disks: "10 GB"
-        container: "ghcr.io/stjudecloud/util:2.1.1"
+        container: "ghcr.io/stjudecloud/util:2.1.2"
         maxRetries: 1
     }
 }
@@ -187,7 +187,7 @@ task calc_gene_lengths {
     runtime {
         memory: "16 GB"
         disks: "~{disk_size_gb} GB"
-        container: "ghcr.io/stjudecloud/util:2.1.1"
+        container: "ghcr.io/stjudecloud/util:2.1.2"
         maxRetries: 1
     }
 }
@@ -313,7 +313,7 @@ task unpack_tarball {
     runtime {
         memory: "4 GB"
         disks: "~{disk_size_gb} GB"
-        container: "ghcr.io/stjudecloud/util:2.1.1"
+        container: "ghcr.io/stjudecloud/util:2.1.2"
         maxRetries: 1
     }
 }
@@ -419,7 +419,7 @@ task global_phred_scores {
     runtime {
         memory: "4 GB"
         disks: "~{disk_size_gb} GB"
-        container: "ghcr.io/stjudecloud/util:2.1.1"
+        container: "ghcr.io/stjudecloud/util:2.1.2"
         maxRetries: 1
     }
 }
@@ -497,7 +497,7 @@ task qc_summary {
     runtime {
         memory: "4 GB"
         disks: "10 GB"
-        container: "ghcr.io/stjudecloud/util:2.1.1"
+        container: "ghcr.io/stjudecloud/util:2.1.2"
         maxRetries: 1
     }
 }
@@ -561,7 +561,7 @@ task split_fastq {
         cpu: ncpu
         memory: "4 GB"
         disks: "~{disk_size_gb} GB"
-        container: "ghcr.io/stjudecloud/util:2.1.1"
+        container: "ghcr.io/stjudecloud/util:2.1.2"
         maxRetries: 1
     }
 }
diff --git a/workflows/dnaseq/dnaseq-standard-fastq.wdl b/workflows/dnaseq/dnaseq-standard-fastq.wdl
@@ -138,7 +138,7 @@ task parse_input {
     }
 
     input {
-        #@ except: DisallowedDeclarationName
+        #@ except: DeclarationName
         Array[Int] array_lengths
         String aligner
     }
@@ -168,7 +168,7 @@ task parse_input {
     runtime {
         memory: "4 GB"
         disks: "10 GB"
-        container: "ghcr.io/stjudecloud/util:2.1.1"
+        container: "ghcr.io/stjudecloud/util:2.1.2"
         maxRetries: 0
     }
 }
diff --git a/workflows/dnaseq/dnaseq-standard.wdl b/workflows/dnaseq/dnaseq-standard.wdl
@@ -136,7 +136,7 @@ task parse_input {
     runtime {
         memory: "4 GB"
         disks: "10 GB"
-        container: "ghcr.io/stjudecloud/util:2.1.1"
+        container: "ghcr.io/stjudecloud/util:2.1.2"
         maxRetries: 0
     }
 }
diff --git a/workflows/qc/quality-check-standard.wdl b/workflows/qc/quality-check-standard.wdl
@@ -557,7 +557,7 @@ task parse_input {
     runtime {
         memory: "4 GB"
         disks: "10 GB"
-        container: "ghcr.io/stjudecloud/util:2.1.1"
+        container: "ghcr.io/stjudecloud/util:2.1.2"
         maxRetries: 1
     }
 }
diff --git a/workflows/rnaseq/rnaseq-standard.wdl b/workflows/rnaseq/rnaseq-standard.wdl
@@ -179,7 +179,7 @@ task parse_input {
     runtime {
         memory: "4 GB"
         disks: "10 GB"
-        container: "ghcr.io/stjudecloud/util:2.1.1"
+        container: "ghcr.io/stjudecloud/util:2.1.2"
         maxRetries: 1
     }
 }

Original file line number	Diff line number	Diff line change
`@@ -118,7 +118,7 @@ task validate_string_is_12bit_oct_dec_or_hex {`
`118`	`118`	`runtime {`
`119`	`119`	`memory: "4 GB"`
`120`	`120`	`disks: "10 GB"`
`121`		`- container: "ghcr.io/stjudecloud/util:2.1.1"`
	`121`	`+ container: "ghcr.io/stjudecloud/util:2.1.2"`
`122`	`122`	`maxRetries: 1`
`123`	`123`	`}`
`124`	`124`	`}`
Original file line number	Diff line number	Diff line change
`@@ -104,7 +104,7 @@ task read_group_to_string {`
`104`	`104`	`runtime {`
`105`	`105`	`memory: "4 GB"`
`106`	`106`	`disks: "10 GB"`
`107`		`- container: "ghcr.io/stjudecloud/util:2.1.1"`
	`107`	`+ container: "ghcr.io/stjudecloud/util:2.1.2"`
`108`	`108`	`maxRetries: 1`
`109`	`109`	`}`
`110`	`110`	`}`
`@@ -441,7 +441,7 @@ task validate_read_group {`
`441`	`441`	`runtime {`
`442`	`442`	`memory: "4 GB"`
`443`	`443`	`disks: "10 GB"`
`444`		`- container: "ghcr.io/stjudecloud/util:2.1.1"`
	`444`	`+ container: "ghcr.io/stjudecloud/util:2.1.2"`
`445`	`445`	`maxRetries: 0`
`446`	`446`	`}`
`447`	`447`	`}`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`	`1`	`{`
`2`	`2`	`"name": "util",`
`3`		`- "version": "2.1.1"`
	`3`	`+ "version": "2.1.2"`
`4`	`4`	`}`
Original file line number	Diff line number	Diff line change
`@@ -209,7 +209,7 @@ task calc_tpm {`
`209`	`209`	`runtime {`
`210`	`210`	`memory: "4 GB"`
`211`	`211`	`disks: "10 GB"`
`212`		`- container: "ghcr.io/stjudecloud/util:2.1.1"`
	`212`	`+ container: "ghcr.io/stjudecloud/util:2.1.2"`
`213`	`213`	`maxRetries: 1`
`214`	`214`	`}`
`215`	`215`	`}`
Original file line number	Diff line number	Diff line change
`@@ -36,7 +36,7 @@ task compute_checksum {`
`36`	`36`	`runtime {`
`37`	`37`	`memory: "4 GB"`
`38`	`38`	`disks: "~{disk_size_gb} GB"`
`39`		`- container: "ghcr.io/stjudecloud/util:2.1.1"`
	`39`	`+ container: "ghcr.io/stjudecloud/util:2.1.2"`
`40`	`40`	`maxRetries: 1`
`41`	`41`	`}`
`42`	`42`	`}`
Original file line number	Diff line number	Diff line change
`@@ -807,7 +807,7 @@ task quality_score_distribution {`
`807`	`807`	`}`
`808`	`808`	`}`
`809`	`809`
`810`		`-#@ except: NonmatchingOutput`
	`810`	`+#@ except: MatchingOutputMeta`
`811`	`811`	`task bam_to_fastq {`
`812`	`812`	`meta {`
`813`	`813`	description: "[Deprecated] This WDL task converts the input BAM file into FASTQ format files. This task has been deprecated in favor of `samtools.bam_to_fastq` which is more performant and doesn't error on 'illegal mate states'."
Original file line number	Diff line number	Diff line change
`@@ -91,7 +91,7 @@ task rnaseq {`
`91`	`91`	`}`
`92`	`92`	`}`
`93`	`93`
`94`		`-#@ except: NonmatchingOutput`
	`94`	`+#@ except: MatchingOutputMeta`
`95`	`95`	`task bamqc {`
`96`	`96`	`meta {`
`97`	`97`	`description: "[Deprecated] This WDL task runs QualiMap's bamqc tool on the input BAM file. This task has been deprecated due to memory leak issues. Use at your own risk, for some samples can consume over 1TB of RAM."`
Original file line number	Diff line number	Diff line change
`@@ -1166,7 +1166,7 @@ task position_sorted_fixmate {`
`1166`	`1166`	`}`
`1167`	`1167`	`}`
`1168`	`1168`
`1169`		`-#@ except: NonmatchingOutput`
	`1169`	`+#@ except: MatchingOutputMeta`
`1170`	`1170`	`task markdup {`
`1171`	`1171`	`meta {`
`1172`	`1172`	description: "[DEPRECATED] Runs `samtools markdup` on the position-sorted input BAM file. This creates a report and optionally a new BAM with duplicate reads marked."
Original file line number	Diff line number	Diff line change
`@@ -42,7 +42,7 @@ task download {`
`42`	`42`	`runtime {`
`43`	`43`	`memory: "4 GB"`
`44`	`44`	`disks: "~{disk_size_gb} GB"`
`45`		`- container: "ghcr.io/stjudecloud/util:2.1.1"`
	`45`	`+ container: "ghcr.io/stjudecloud/util:2.1.2"`
`46`	`46`	`maxRetries: 1`
`47`	`47`	`}`
`48`	`48`	`}`
`@@ -139,7 +139,7 @@ task split_string {`
`139`	`139`	`runtime {`
`140`	`140`	`memory: "4 GB"`
`141`	`141`	`disks: "10 GB"`
`142`		`- container: "ghcr.io/stjudecloud/util:2.1.1"`
	`142`	`+ container: "ghcr.io/stjudecloud/util:2.1.2"`
`143`	`143`	`maxRetries: 1`
`144`	`144`	`}`
`145`	`145`	`}`
`@@ -187,7 +187,7 @@ task calc_gene_lengths {`
`187`	`187`	`runtime {`
`188`	`188`	`memory: "16 GB"`
`189`	`189`	`disks: "~{disk_size_gb} GB"`
`190`		`- container: "ghcr.io/stjudecloud/util:2.1.1"`
	`190`	`+ container: "ghcr.io/stjudecloud/util:2.1.2"`
`191`	`191`	`maxRetries: 1`
`192`	`192`	`}`
`193`	`193`	`}`
`@@ -313,7 +313,7 @@ task unpack_tarball {`
`313`	`313`	`runtime {`
`314`	`314`	`memory: "4 GB"`
`315`	`315`	`disks: "~{disk_size_gb} GB"`
`316`		`- container: "ghcr.io/stjudecloud/util:2.1.1"`
	`316`	`+ container: "ghcr.io/stjudecloud/util:2.1.2"`
`317`	`317`	`maxRetries: 1`
`318`	`318`	`}`
`319`	`319`	`}`
`@@ -419,7 +419,7 @@ task global_phred_scores {`
`419`	`419`	`runtime {`
`420`	`420`	`memory: "4 GB"`
`421`	`421`	`disks: "~{disk_size_gb} GB"`
`422`		`- container: "ghcr.io/stjudecloud/util:2.1.1"`
	`422`	`+ container: "ghcr.io/stjudecloud/util:2.1.2"`
`423`	`423`	`maxRetries: 1`
`424`	`424`	`}`
`425`	`425`	`}`
`@@ -497,7 +497,7 @@ task qc_summary {`
`497`	`497`	`runtime {`
`498`	`498`	`memory: "4 GB"`
`499`	`499`	`disks: "10 GB"`
`500`		`- container: "ghcr.io/stjudecloud/util:2.1.1"`
	`500`	`+ container: "ghcr.io/stjudecloud/util:2.1.2"`
`501`	`501`	`maxRetries: 1`
`502`	`502`	`}`
`503`	`503`	`}`
`@@ -561,7 +561,7 @@ task split_fastq {`
`561`	`561`	`cpu: ncpu`
`562`	`562`	`memory: "4 GB"`
`563`	`563`	`disks: "~{disk_size_gb} GB"`
`564`		`- container: "ghcr.io/stjudecloud/util:2.1.1"`
	`564`	`+ container: "ghcr.io/stjudecloud/util:2.1.2"`
`565`	`565`	`maxRetries: 1`
`566`	`566`	`}`
`567`	`567`	`}`
Original file line number	Diff line number	Diff line change
`@@ -138,7 +138,7 @@ task parse_input {`
`138`	`138`	`}`
`139`	`139`
`140`	`140`	`input {`
`141`		`- #@ except: DisallowedDeclarationName`
	`141`	`+ #@ except: DeclarationName`
`142`	`142`	`Array[Int] array_lengths`
`143`	`143`	`String aligner`
`144`	`144`	`}`
`@@ -168,7 +168,7 @@ task parse_input {`
`168`	`168`	`runtime {`
`169`	`169`	`memory: "4 GB"`
`170`	`170`	`disks: "10 GB"`
`171`		`- container: "ghcr.io/stjudecloud/util:2.1.1"`
	`171`	`+ container: "ghcr.io/stjudecloud/util:2.1.2"`
`172`	`172`	`maxRetries: 0`
`173`	`173`	`}`
`174`	`174`	`}`