Merge pull request #543 from umccr/enhancement/remove-tmpdir-from-qua…

…limap Remove tmpdir option in qualimap
umccr · Jul 31, 2024 · 044f8d0 · 044f8d0
2 parents a4564f8 + b832aa7
commit 044f8d0
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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: a102e993fed3fe5efd3833b9f2221df9
+> md5sum: f1abbae5449aa241845532350d577b55
 
 ### qualimap v(2.2.2) documentation
 
@@ -128,20 +128,6 @@ Sequencing library protocol:
 strand-specific-forward, strand-specific-reverse or 
 non-strand-specific (default).
 
-
-### tmp dir
-
-
-
-
-> ID: tmp_dir
-  
-**Optional:** `True`  
-**Type:** `string`  
-**Docs:**  
-Qualimap creates temporary bam files when sorting by name, which takes up space in the system tmp dir (usually /tmp). 
-This can be avoided by sorting the bam file by name before running Qualimap.
-
 
 
 

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: 3b64c5f5939b734bce46a82483d01525
+> md5sum: b3855ac8040a148badc29bb04d92ba54
 
 ### dragen-transcriptome-pipeline v(3.9.3) documentation
 
@@ -369,20 +369,6 @@ you would like to use. To disable soft trimming, set to none. During mapping, re
 and bases are not removed from the reads. Soft-trimming is enabled for the polyg filter by default.
 
 
-### tmp dir
-
-
-
-
-> ID: tmp_dir
-  
-**Optional:** `True`  
-**Type:** `string`  
-**Docs:**  
-Qualimap creates temporary bam files when sorting by name, which takes up space in the system tmp dir (usually /tmp). 
-This can be avoided by sorting the bam file by name before running Qualimap.
-
-
 ### trim adapter r1 5prime
 
 
@@ -1138,7 +1124,7 @@ bash wfr.491f5fd1b5e74f6e87113d964675504e.launch.sh
 
 
 **workflow name:** dragen-transcriptome-pipeline_prod-wf  
-**wfl version name:** 3.9.3--d7f9749  
+**wfl version name:** 3.9.3--0ac1f6a  
 
 
 
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: 4e946045ad3fc9fef3c4953e1d47d558
+> md5sum: d67c5240620328cde6e35aae5d106a72
 
 ### dragen-transcriptome-pipeline v(4.0.3) documentation
 
@@ -376,20 +376,6 @@ FastA file with genome sequence
 **Docs:**  
 Path to ref data tarball
 
-
-### tmp dir
-
-
-
-
-> ID: tmp_dir
-  
-**Optional:** `True`  
-**Type:** `string`  
-**Docs:**  
-Qualimap creates temporary bam files when sorting by name, which takes up space in the system tmp dir (usually /tmp). 
-This can be avoided by sorting the bam file by name before running Qualimap.
-
 
 
 
@@ -605,7 +591,7 @@ The output directory containing all transcriptome output files
 
 
 **workflow name:** dragen-transcriptome-pipeline_prod-wf  
-**wfl version name:** 4.0.3--81f95bd  
+**wfl version name:** 4.0.3--0ac1f6a  
 
 
 
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: b44e61f6be9e017e154a19eefcb4e42d
+> md5sum: b63aaf8d3b9fc4800cdd1fbd26a55772
 
 ### dragen-transcriptome-pipeline v(4.2.4) documentation
 
@@ -407,20 +407,6 @@ you would like to use. To disable soft trimming, set to none. During mapping, re
 and bases are not removed from the reads. Soft-trimming is enabled for the polyg filter by default.
 
 
-### tmp dir
-
-
-
-
-> ID: tmp_dir
-  
-**Optional:** `True`  
-**Type:** `string`  
-**Docs:**  
-Qualimap creates temporary bam files when sorting by name, which takes up space in the system tmp dir (usually /tmp). 
-This can be avoided by sorting the bam file by name before running Qualimap.
-
-
 ### trim adapter r1 5prime
 
 
@@ -754,7 +740,7 @@ The output directory containing all transcriptome output files
 
 
 **workflow name:** dragen-transcriptome-pipeline_prod-wf  
-**wfl version name:** 4.2.4--81f95bd  
+**wfl version name:** 4.2.4--0ac1f6a  
 
 
 
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: 96a7ab0527e74ed86c34a76a832f5377
+> md5sum: 20cdbee2575c25ec84a6f9852a6b409c
 
 ### dragen-wts-qc-pipeline v(3.9.3) documentation
 
@@ -229,20 +229,6 @@ The prefix given to all output files
 **Docs:**  
 Path to ref data tarball
 
-
-### tmp dir
-
-
-
-
-> ID: tmp_dir
-  
-**Optional:** `True`  
-**Type:** `string`  
-**Docs:**  
-Qualimap creates temporary bam files when sorting by name, which takes up space in the system tmp dir (usually /tmp). 
-This can be avoided by sorting the bam file by name before running Qualimap.
-
 
 
 

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: c642c44a7be068bd133d2c9ea80bcb67
+> md5sum: d80801b9105b2843d6c9d46881419942
 
 ### dragen-wts-qc-pipeline v(4.0.3) documentation
 
@@ -266,20 +266,6 @@ The prefix given to all output files
 **Docs:**  
 Path to ref data tarball
 
-
-### tmp dir
-
-
-
-
-> ID: tmp_dir
-  
-**Optional:** `True`  
-**Type:** `string`  
-**Docs:**  
-Qualimap creates temporary bam files when sorting by name, which takes up space in the system tmp dir (usually /tmp). 
-This can be avoided by sorting the bam file by name before running Qualimap.
-
 
 
 

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: a82294d17eb4fd0cea53d7d48ffdd8a6
+> md5sum: d4939a3d60c5347d0be5149f325e262f
 
 ### dragen-wts-qc-pipeline v(4.2.4) documentation
 
@@ -266,20 +266,6 @@ The prefix given to all output files
 **Docs:**  
 Path to ref data tarball
 
-
-### tmp dir
-
-
-
-
-> ID: tmp_dir
-  
-**Optional:** `True`  
-**Type:** `string`  
-**Docs:**  
-Qualimap creates temporary bam files when sorting by name, which takes up space in the system tmp dir (usually /tmp). 
-This can be avoided by sorting the bam file by name before running Qualimap.
-