From 7b61f425ba44eb3d9748eed88bcb21a9eda6f288 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Thu, 9 May 2024 03:28:00 +0000 Subject: [PATCH] site deploy Auto-generated via {sandpaper} Source : 2aa92ed2992deff3fda5ad5411ef5cadcb5f8b79 Branch : md-outputs Author : GitHub Actions Time : 2024-05-09 03:27:46 +0000 Message : markdown source builds Auto-generated via {sandpaper} Source : 72ba75fe9fe827209821d7230a8d6757469ec66a Branch : main Author : Alexis Lucattini Time : 2024-05-09 03:24:58 +0000 Message : Merge pull request #31 from umccr/bugfix/commit-bio-cwl-tools Commit bio-cwl-tools --- 03-dependency_graphs.html | 14 +++++------- 04-reusing_tools.html | 10 ++++---- addendum-01-debug.html | 10 ++++---- aio.html | 34 +++++++++++++--------------- instructor/03-dependency_graphs.html | 14 +++++------- instructor/04-reusing_tools.html | 10 ++++---- instructor/addendum-01-debug.html | 10 ++++---- instructor/aio.html | 34 +++++++++++++--------------- md5sum.txt | 2 +- 9 files changed, 65 insertions(+), 73 deletions(-) diff --git a/03-dependency_graphs.html b/03-dependency_graphs.html index a221815..d785166 100644 --- a/03-dependency_graphs.html +++ b/03-dependency_graphs.html @@ -519,25 +519,23 @@

BASH -


-
+
-
-

Should we be concerned about this warning -๐ŸŒถ๐ŸŒถ๐ŸŒถ +
+

Whatโ€™s in a warning ๐ŸŒถ๐ŸŒถ๐ŸŒถ

-

Not all warnings are bad.
-Should we be concerned about this warning? If not, why not?

+

Should we be concerned about this warning?

+

If not, why not?

diff --git a/04-reusing_tools.html b/04-reusing_tools.html index 527cf21..571bc2f 100644 --- a/04-reusing_tools.html +++ b/04-reusing_tools.html @@ -342,7 +342,7 @@

Find the featureCounts tool in the -
+

The featureCounts CWL document can be found in the GitHub repo.

@@ -390,7 +390,7 @@

Add the featureCounts tool to the workflow -
+

Use the run field to add the featureCounts tool as a step in the workflow.

@@ -403,7 +403,7 @@

Hint: Feature Counts Workflow Ste -
+

Use a requirements entry with ResourceRequirement to allocate a ramMin of @@ -417,7 +417,7 @@

Hint: Upgrade RAM

-
+

YAML @@ -515,7 +515,7 @@

YAML
workflow_input_3.yml (Click to expand)

-
+

YAML diff --git a/addendum-01-debug.html b/addendum-01-debug.html index 8c9eebc..1f5ec8d 100644 --- a/addendum-01-debug.html +++ b/addendum-01-debug.html @@ -368,7 +368,7 @@

BASH
Show details

-
+
ERROR Tool definition failed validation:
 while scanning for the next token
@@ -442,7 +442,7 @@ 
BASH
 
CWLTOOL VALIDATE ERROR MESSAGE

 
-

+

 

 
ERROR Tool definition failed validation:
 rna_seq_workflow_fieldname_fail.cwl:1:1:   Object `rna_seq_workflow_fieldname_fail.cwl` is not valid
@@ -535,7 +535,7 @@ 
BASH
 
CWLTOOL VALIDATE ERROR MESSAGE

 
-

+

 

 
ERROR Tool definition failed validation:
 rna_seq_workflow_varname_fail.cwl:8:1:  checking field `steps`
@@ -658,7 +658,7 @@ 
BASH
 
Incompatible type cwltool error message

 
-

+

 

 
rna_seq_workflow_type_fail.cwl:5:3:   Source 'rna_reads_fruitfly' of type "int" is incompatible
 rna_seq_workflow_type_fail.cwl:12:7:   with sink 'reads_file' of type "File"
@@ -761,7 +761,7 @@ 
BASH
 
Incompatible format error message

 
-

+

 

 
ERROR Exception on step 'mapping_reads'
 ERROR [step mapping_reads] Cannot make job: Expected value of 'ForwardReads' to have format http://edamontology.org/format_1930 but
diff --git a/aio.html b/aio.html
index 775ae62..b41320a 100644
--- a/aio.html
+++ b/aio.html
@@ -1620,25 +1620,23 @@ 
BASH

-


-

+

 

 
 

-

-
Should we be concerned about this warning
-๐ŸŒถ๐ŸŒถ๐ŸŒถ
+

+
Whatโ€™s in a warning ๐ŸŒถ๐ŸŒถ๐ŸŒถ
 

 

-
Not all warnings are bad.

-Should we be concerned about this warning? If not, why not?

+
Should we be concerned about this warning?

+
If not, why not?

 

 

 

 

 

 
 

 

@@ -1975,7 +1973,7 @@ 
Find the featureCounts tool in the
 
-

+

 

 
The featureCounts CWL document can be found in the GitHub
 repo.

@@ -2024,7 +2022,7 @@ 
Add the featureCounts tool to the workflow
 
-

+

 

 
Use the run field to add the featureCounts
 tool as a step in the workflow.

@@ -2037,7 +2035,7 @@ 
Hint: Feature Counts Workflow Ste
 
-

+

 

 
Use a requirements entry with
 ResourceRequirement to allocate a ramMin of
@@ -2051,7 +2049,7 @@ 
Hint: Upgrade RAM

 
-

+

 

 

 
YAML
@@ -2150,7 +2148,7 @@ 
YAML
 
workflow_input_3.yml (Click to expand)

 
-

+

 

 

 
YAML
@@ -2308,7 +2306,7 @@ 
BASH
 
Show details

 
-

+

 

 
ERROR Tool definition failed validation:
 while scanning for the next token
@@ -2383,7 +2381,7 @@ 
BASH
 
CWLTOOL VALIDATE ERROR MESSAGE

 
-

+

 

 
ERROR Tool definition failed validation:
 rna_seq_workflow_fieldname_fail.cwl:1:1:   Object `rna_seq_workflow_fieldname_fail.cwl` is not valid
@@ -2477,7 +2475,7 @@ 
BASH
 
CWLTOOL VALIDATE ERROR MESSAGE

 
-

+

 

 
ERROR Tool definition failed validation:
 rna_seq_workflow_varname_fail.cwl:8:1:  checking field `steps`
@@ -2602,7 +2600,7 @@ 
BASH
 
Incompatible type cwltool error message

 
-

+

 

 
rna_seq_workflow_type_fail.cwl:5:3:   Source 'rna_reads_fruitfly' of type "int" is incompatible
 rna_seq_workflow_type_fail.cwl:12:7:   with sink 'reads_file' of type "File"
@@ -2706,7 +2704,7 @@ 
BASH
 
Incompatible format error message

 
-

+

 

 
ERROR Exception on step 'mapping_reads'
 ERROR [step mapping_reads] Cannot make job: Expected value of 'ForwardReads' to have format http://edamontology.org/format_1930 but
diff --git a/instructor/03-dependency_graphs.html b/instructor/03-dependency_graphs.html
index 3ff8b8e..f54cbc2 100644
--- a/instructor/03-dependency_graphs.html
+++ b/instructor/03-dependency_graphs.html
@@ -520,25 +520,23 @@ 
BASH

-


-

+

 

 
 

-

-
Should we be concerned about this warning
-๐ŸŒถ๐ŸŒถ๐ŸŒถ
+

+
Whatโ€™s in a warning ๐ŸŒถ๐ŸŒถ๐ŸŒถ
 

 

-
Not all warnings are bad.

-Should we be concerned about this warning? If not, why not?

+
Should we be concerned about this warning?

+
If not, why not?

 

 

 

 

 

 
 

 

diff --git a/instructor/04-reusing_tools.html b/instructor/04-reusing_tools.html
index 4aa945b..17c8901 100644
--- a/instructor/04-reusing_tools.html
+++ b/instructor/04-reusing_tools.html
@@ -343,7 +343,7 @@ 
Find the featureCounts tool in the
 
-

+

 

 
The featureCounts CWL document can be found in the GitHub
 repo.

@@ -391,7 +391,7 @@ 
Add the featureCounts tool to the workflow
 
-

+

 

 
Use the run field to add the featureCounts
 tool as a step in the workflow.

@@ -404,7 +404,7 @@ 
Hint: Feature Counts Workflow Ste
 
-

+

 

 
Use a requirements entry with
 ResourceRequirement to allocate a ramMin of
@@ -418,7 +418,7 @@ 
Hint: Upgrade RAM

 
-

+

 

 

 
YAML
@@ -516,7 +516,7 @@ 
YAML
 
workflow_input_3.yml (Click to expand)

 
-

+

 

 

 
YAML
diff --git a/instructor/addendum-01-debug.html b/instructor/addendum-01-debug.html
index 1186a0c..d798536 100644
--- a/instructor/addendum-01-debug.html
+++ b/instructor/addendum-01-debug.html
@@ -369,7 +369,7 @@ 
BASH
 
Show details

 
-

+

 

 
ERROR Tool definition failed validation:
 while scanning for the next token
@@ -443,7 +443,7 @@ 
BASH
 
CWLTOOL VALIDATE ERROR MESSAGE

 
-

+

 

 
ERROR Tool definition failed validation:
 rna_seq_workflow_fieldname_fail.cwl:1:1:   Object `rna_seq_workflow_fieldname_fail.cwl` is not valid
@@ -536,7 +536,7 @@ 
BASH
 
CWLTOOL VALIDATE ERROR MESSAGE

 
-

+

 

 
ERROR Tool definition failed validation:
 rna_seq_workflow_varname_fail.cwl:8:1:  checking field `steps`
@@ -659,7 +659,7 @@ 
BASH
 
Incompatible type cwltool error message

 
-

+

 

 
rna_seq_workflow_type_fail.cwl:5:3:   Source 'rna_reads_fruitfly' of type "int" is incompatible
 rna_seq_workflow_type_fail.cwl:12:7:   with sink 'reads_file' of type "File"
@@ -762,7 +762,7 @@ 
BASH
 
Incompatible format error message

 
-

+

 

 
ERROR Exception on step 'mapping_reads'
 ERROR [step mapping_reads] Cannot make job: Expected value of 'ForwardReads' to have format http://edamontology.org/format_1930 but
diff --git a/instructor/aio.html b/instructor/aio.html
index d97bddc..cd17774 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -1640,25 +1640,23 @@ 
BASH

-


-

+

 

 
 

-

-
Should we be concerned about this warning
-๐ŸŒถ๐ŸŒถ๐ŸŒถ
+

+
Whatโ€™s in a warning ๐ŸŒถ๐ŸŒถ๐ŸŒถ
 

 

-
Not all warnings are bad.

-Should we be concerned about this warning? If not, why not?

+
Should we be concerned about this warning?

+
If not, why not?

 

 

 

 

 

 
 

 

@@ -1996,7 +1994,7 @@ 
Find the featureCounts tool in the
 
-

+

 

 
The featureCounts CWL document can be found in the GitHub
 repo.

@@ -2045,7 +2043,7 @@ 
Add the featureCounts tool to the workflow
 
-

+

 

 
Use the run field to add the featureCounts
 tool as a step in the workflow.

@@ -2058,7 +2056,7 @@ 
Hint: Feature Counts Workflow Ste
 
-

+

 

 
Use a requirements entry with
 ResourceRequirement to allocate a ramMin of
@@ -2072,7 +2070,7 @@ 
Hint: Upgrade RAM

 
-

+

 

 

 
YAML
@@ -2171,7 +2169,7 @@ 
YAML
 
workflow_input_3.yml (Click to expand)

 
-

+

 

 

 
YAML
@@ -2330,7 +2328,7 @@ 
BASH
 
Show details

 
-

+

 

 
ERROR Tool definition failed validation:
 while scanning for the next token
@@ -2405,7 +2403,7 @@ 
BASH
 
CWLTOOL VALIDATE ERROR MESSAGE

 
-

+

 

 
ERROR Tool definition failed validation:
 rna_seq_workflow_fieldname_fail.cwl:1:1:   Object `rna_seq_workflow_fieldname_fail.cwl` is not valid
@@ -2499,7 +2497,7 @@ 
BASH
 
CWLTOOL VALIDATE ERROR MESSAGE

 
-

+

 

 
ERROR Tool definition failed validation:
 rna_seq_workflow_varname_fail.cwl:8:1:  checking field `steps`
@@ -2624,7 +2622,7 @@ 
BASH
 
Incompatible type cwltool error message

 
-

+

 

 
rna_seq_workflow_type_fail.cwl:5:3:   Source 'rna_reads_fruitfly' of type "int" is incompatible
 rna_seq_workflow_type_fail.cwl:12:7:   with sink 'reads_file' of type "File"
@@ -2728,7 +2726,7 @@ 
BASH
 
Incompatible format error message

 
-

+

 

 
ERROR Exception on step 'mapping_reads'
 ERROR [step mapping_reads] Cannot make job: Expected value of 'ForwardReads' to have format http://edamontology.org/format_1930 but
diff --git a/md5sum.txt b/md5sum.txt
index cc1cf8e..1cc823d 100644
--- a/md5sum.txt
+++ b/md5sum.txt
@@ -6,7 +6,7 @@
 "links.md" "8184cf4149eafbf03ce8da8ff0778c14" "site/built/links.md" "2024-05-09"
 "episodes/01-introduction.Rmd" "d32b6b5562a66dc90d79acbf60210375" "site/built/01-introduction.md" "2024-05-09"
 "episodes/02-shell_to_cwl.Rmd" "9d08ba8ae7875dee96e8f80de70907ea" "site/built/02-shell_to_cwl.md" "2024-05-09"
-"episodes/03-dependency_graphs.Rmd" "f55a067639c7f056312d9e137fdf2ed6" "site/built/03-dependency_graphs.md" "2024-05-09"
+"episodes/03-dependency_graphs.Rmd" "e992b9ccbd2fb1d8a1a5f6e1d4b2fc18" "site/built/03-dependency_graphs.md" "2024-05-09"
 "episodes/04-reusing_tools.Rmd" "4a90245e02110dbb13296102d3ce75a2" "site/built/04-reusing_tools.md" "2024-05-09"
 "episodes/addendum-01-debug.Rmd" "3ce548abd8cb1934aa12b16cd62104e3" "site/built/addendum-01-debug.md" "2024-05-09"
 "episodes/more_info.md" "b97f3b7186f568f33352041b7e2449ff" "site/built/more_info.md" "2024-05-09"