Merge pull request #548 from umccr/bugfix/rollback-scratch-space

Qualimap should use scratch directory if it exists, otherwise resort to tmp
umccr · Aug 3, 2024 · 7af9101 · 7af9101
2 parents fb44017 + 4b42efe
commit 7af9101
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diff --git a/.github/catalogue/docs/tools/dragen-somatic/4.2.4/dragen-somatic__4.2.4.md b/.github/catalogue/docs/tools/dragen-somatic/4.2.4/dragen-somatic__4.2.4.md
@@ -17,7 +17,7 @@ dragen-somatic 4.2.4 tool
 
 
 > ID: dragen-somatic--4.2.4  
-> md5sum: 833e6305bad43d281aec9ef3909e8e74
+> md5sum: 56c5a9a13a722e8593c4448039cba61d
 
 ### dragen-somatic v(4.2.4) documentation
 
@@ -1237,7 +1237,7 @@ Enables the multiallelic filter. The default is true.
 > ID: vc_enable_unequal_ntd
   
 **Optional:** `True`  
-**Type:** `['boolean', <cwl_utils.parser.cwl_v1_1.CommandInputEnumSchema object at 0x7f9ed06a1070>]`  
+**Type:** `['boolean', <cwl_utils.parser.cwl_v1_1.CommandInputEnumSchema object at 0x7f6f39b6ed50>]`  
 **Docs:**  
 Nucleotide (NTD) Error Bias Estimation is on by default and recommended as a replacement for the orientation bias filter.
 Both methods take account of strand-specific biases (systematic differences between F1R2 and F2R1 reads).

diff --git a/.github/catalogue/docs/tools/qualimap/2.2.2/qualimap__2.2.2.md b/.github/catalogue/docs/tools/qualimap/2.2.2/qualimap__2.2.2.md
@@ -17,7 +17,7 @@ qualimap 2.2.2 tool
 
 
 > ID: qualimap--2.2.2  
-> md5sum: f1abbae5449aa241845532350d577b55
+> md5sum: c6eae8729c871bc8bf5f3ae0ee64e0e4
 
 ### qualimap v(2.2.2) documentation
 

diff --git a/.../docs/workflows/dragen-somatic-pipeline/4.2.4/dragen-somatic-pipeline__4.2.4.md b/.../docs/workflows/dragen-somatic-pipeline/4.2.4/dragen-somatic-pipeline__4.2.4.md
@@ -19,7 +19,7 @@ dragen-somatic-pipeline 4.2.4 workflow
 
 
 > ID: dragen-somatic-pipeline--4.2.4  
-> md5sum: 6c7445d9a17ae6ffe6f411312383e87e
+> md5sum: d17f4493e61c1f6b0467067c6b1322dc
 
 ### dragen-somatic-pipeline v(4.2.4) documentation
 
@@ -1202,7 +1202,7 @@ Enables the multiallelic filter. The default is true.
 > ID: vc_enable_unequal_ntd
   
 **Optional:** `True`  
-**Type:** `['boolean', <cwl_utils.parser.cwl_v1_1.InputEnumSchema object at 0x7f097379ae10>]`  
+**Type:** `['boolean', <cwl_utils.parser.cwl_v1_1.InputEnumSchema object at 0x7eff40a2f2c0>]`  
 **Docs:**  
 Nucleotide (NTD) Error Bias Estimation is on by default and recommended as a replacement for the orientation bias filter.
 Both methods take account of strand-specific biases (systematic differences between F1R2 and F2R1 reads).
@@ -1660,7 +1660,7 @@ Bam file of the tumor sample
 
 
 **workflow name:** dragen-somatic-pipeline_prod-wf  
-**wfl version name:** 4.2.4--81f95bd  
+**wfl version name:** 4.2.4--a9cc9b5  
 
 
 
diff --git a/...ic-with-germline-pipeline/4.2.4/dragen-somatic-with-germline-pipeline__4.2.4.md b/...ic-with-germline-pipeline/4.2.4/dragen-somatic-with-germline-pipeline__4.2.4.md
@@ -19,7 +19,7 @@ dragen-somatic-with-germline-pipeline 4.2.4 workflow
 
 
 > ID: dragen-somatic-with-germline-pipeline--4.2.4  
-> md5sum: d4b38cae611fe37681c02d03606ab3cd
+> md5sum: 2418c871a226483ee9bf79b9cbe66253
 
 ### dragen-somatic-with-germline-pipeline v(4.2.4) documentation
 
@@ -1483,7 +1483,7 @@ Enables the multiallelic filter. The default is true.
 > ID: vc_enable_unequal_ntd
   
 **Optional:** `True`  
-**Type:** `['boolean', <cwl_utils.parser.cwl_v1_1.InputEnumSchema object at 0x7f9813b124e0>]`  
+**Type:** `['boolean', <cwl_utils.parser.cwl_v1_1.InputEnumSchema object at 0x7f2edafa4ef0>]`  
 **Docs:**  
 Nucleotide (NTD) Error Bias Estimation is on by default and recommended as a replacement for the orientation bias filter.
 Both methods take account of strand-specific biases (systematic differences between F1R2 and F2R1 reads).
@@ -2029,7 +2029,7 @@ Bam file of the tumor sample
 
 
 **workflow name:** dragen-somatic-with-germline-pipeline_prod-wf  
-**wfl version name:** 4.2.4--81f95bd  
+**wfl version name:** 4.2.4--a9cc9b5  
 
 
 
diff --git a/...ows/dragen-transcriptome-pipeline/3.9.3/dragen-transcriptome-pipeline__3.9.3.md b/...ows/dragen-transcriptome-pipeline/3.9.3/dragen-transcriptome-pipeline__3.9.3.md
@@ -19,7 +19,7 @@ dragen-transcriptome-pipeline 3.9.3 workflow
 
 
 > ID: dragen-transcriptome-pipeline--3.9.3  
-> md5sum: b3855ac8040a148badc29bb04d92ba54
+> md5sum: f44f16964b77c3649db77f3230d0beef
 
 ### dragen-transcriptome-pipeline v(3.9.3) documentation
 
@@ -1124,7 +1124,7 @@ bash wfr.491f5fd1b5e74f6e87113d964675504e.launch.sh
 
 
 **workflow name:** dragen-transcriptome-pipeline_prod-wf  
-**wfl version name:** 3.9.3--0ac1f6a  
+**wfl version name:** 3.9.3--a9cc9b5  
 
 
 
diff --git a/...ows/dragen-transcriptome-pipeline/4.0.3/dragen-transcriptome-pipeline__4.0.3.md b/...ows/dragen-transcriptome-pipeline/4.0.3/dragen-transcriptome-pipeline__4.0.3.md
@@ -19,7 +19,7 @@ dragen-transcriptome-pipeline 4.0.3 workflow
 
 
 > ID: dragen-transcriptome-pipeline--4.0.3  
-> md5sum: d67c5240620328cde6e35aae5d106a72
+> md5sum: a8e084fa69cfe37d9841e7a711905a92
 
 ### dragen-transcriptome-pipeline v(4.0.3) documentation
 
@@ -591,7 +591,7 @@ The output directory containing all transcriptome output files
 
 
 **workflow name:** dragen-transcriptome-pipeline_prod-wf  
-**wfl version name:** 4.0.3--0ac1f6a  
+**wfl version name:** 4.0.3--a9cc9b5  
 
 
 
diff --git a/...ows/dragen-transcriptome-pipeline/4.2.4/dragen-transcriptome-pipeline__4.2.4.md b/...ows/dragen-transcriptome-pipeline/4.2.4/dragen-transcriptome-pipeline__4.2.4.md
@@ -19,7 +19,7 @@ dragen-transcriptome-pipeline 4.2.4 workflow
 
 
 > ID: dragen-transcriptome-pipeline--4.2.4  
-> md5sum: b63aaf8d3b9fc4800cdd1fbd26a55772
+> md5sum: c142f00004a02ac7d7247c0767ee9ff2
 
 ### dragen-transcriptome-pipeline v(4.2.4) documentation
 
@@ -740,7 +740,7 @@ The output directory containing all transcriptome output files
 
 
 **workflow name:** dragen-transcriptome-pipeline_prod-wf  
-**wfl version name:** 4.2.4--0ac1f6a  
+**wfl version name:** 4.2.4--a9cc9b5  
 
 
 
diff --git a/...ue/docs/workflows/dragen-wts-qc-pipeline/3.9.3/dragen-wts-qc-pipeline__3.9.3.md b/...ue/docs/workflows/dragen-wts-qc-pipeline/3.9.3/dragen-wts-qc-pipeline__3.9.3.md
@@ -19,7 +19,7 @@ dragen-wts-qc-pipeline 3.9.3 workflow
 
 
 > ID: dragen-wts-qc-pipeline--3.9.3  
-> md5sum: 20cdbee2575c25ec84a6f9852a6b409c
+> md5sum: cea1b3bdcffd8af6374837267ae886ab
 
 ### dragen-wts-qc-pipeline v(3.9.3) documentation
 

diff --git a/...ue/docs/workflows/dragen-wts-qc-pipeline/4.0.3/dragen-wts-qc-pipeline__4.0.3.md b/...ue/docs/workflows/dragen-wts-qc-pipeline/4.0.3/dragen-wts-qc-pipeline__4.0.3.md
@@ -19,7 +19,7 @@ dragen-wts-qc-pipeline 4.0.3 workflow
 
 
 > ID: dragen-wts-qc-pipeline--4.0.3  
-> md5sum: d80801b9105b2843d6c9d46881419942
+> md5sum: d70578e8f6acfbea4aa0862645d0985f
 
 ### dragen-wts-qc-pipeline v(4.0.3) documentation
 

diff --git a/...ue/docs/workflows/dragen-wts-qc-pipeline/4.2.4/dragen-wts-qc-pipeline__4.2.4.md b/...ue/docs/workflows/dragen-wts-qc-pipeline/4.2.4/dragen-wts-qc-pipeline__4.2.4.md
@@ -19,7 +19,7 @@ dragen-wts-qc-pipeline 4.2.4 workflow
 
 
 > ID: dragen-wts-qc-pipeline--4.2.4  
-> md5sum: d4939a3d60c5347d0be5149f325e262f
+> md5sum: f37412bb676a8ea2ebbdcf6bc24b62a9
 
 ### dragen-wts-qc-pipeline v(4.2.4) documentation