diff --git a/articles/feature1_constantAttributes.html b/articles/feature1_constantAttributes.html index b0fa3b2..c1d2267 100644 --- a/articles/feature1_constantAttributes.html +++ b/articles/feature1_constantAttributes.html @@ -236,7 +236,7 @@

Code package = "pepr" ) p = Project(projectConfig) -#> Loading config file: /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_append/project_config.yaml +#> Loading config file: /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_append/project_config.yaml

And inspect it:

 sampleTable(p)
@@ -257,7 +257,7 @@ 
Code
 #> Config object. Class: Config
 #>  pep_version: 2.0.0
 #>  sample_table: 
-#> /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_append/sample_table.csv
+#> /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_append/sample_table.csv
 #>  sample_modifiers:
 #>     append:
 #>         read_type: SINGLE
diff --git a/articles/feature2_impliedAttributes.html b/articles/feature2_impliedAttributes.html
index 4304a5a..75b2387 100644
--- a/articles/feature2_impliedAttributes.html
+++ b/articles/feature2_impliedAttributes.html
@@ -311,7 +311,7 @@ 
Code
 package = "pepr"
 )
 p = Project(projectConfig)
-#> Loading config file: /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_imply/project_config.yaml
+#> Loading config file: /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_imply/project_config.yaml

And inspect it:

 sampleTable(p)
@@ -341,9 +341,9 @@ 
Code
 #> Config object. Class: Config
 #>  pep_version: 2.0.0
 #>  sample_table: 
-#> /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_imply/sample_table.csv
+#> /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_imply/sample_table.csv
 #>  looper:
-#>     output_dir: /Users/runner/hello_looper_results
+#>     output_dir: /home/runner/hello_looper_results
 #>  sample_modifiers:
 #>     imply:
 #>             if:
diff --git a/articles/feature3_derivedAttributes.html b/articles/feature3_derivedAttributes.html
index 41ee408..3eb7120 100644
--- a/articles/feature3_derivedAttributes.html
+++ b/articles/feature3_derivedAttributes.html
@@ -254,7 +254,7 @@ 
Code
 package = "pepr"
 )
 p = Project(projectConfig)
-#> Loading config file: /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_derive/project_config.yaml
+#> Loading config file: /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_derive/project_config.yaml

And inspect it:

 sampleTable(p)
@@ -263,11 +263,11 @@ 
Code
 #> 2:      pig_1h     RRBS      pig    1
 #> 3:     frog_0h     RRBS     frog    0
 #> 4:     frog_1h     RRBS     frog    1
-#>                                       file_path
-#> 1:  /Users/runner/data/lab/project/pig_0h.fastq
-#> 2:  /Users/runner/data/lab/project/pig_1h.fastq
-#> 3: /Users/runner/data/lab/project/frog_0h.fastq
-#> 4: /Users/runner/data/lab/project/frog_1h.fastq
+#> file_path +#> 1: /home/runner/data/lab/project/pig_0h.fastq +#> 2: /home/runner/data/lab/project/pig_1h.fastq +#> 3: /home/runner/data/lab/project/frog_0h.fastq +#> 4: /home/runner/data/lab/project/frog_1h.fastq

As you can see, the resulting samples are annotated the same way as if they were read from the original, unwieldy, annotations file.

What is more, the p object consists of all the @@ -279,13 +279,13 @@

Code #> Config object. Class: Config #> pep_version: 2.0.0 #> sample_table: -#> /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_derive/sample_table.csv -#> output_dir: /Users/runner/hello_looper_results +#> /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_derive/sample_table.csv +#> output_dir: /home/runner/hello_looper_results #> sample_modifiers: #> derive: #> attributes: file_path #> sources: -#> source1: /Users/runner/data/lab/project/{organism}_{time}h.fastq +#> source1: /home/runner/data/lab/project/{organism}_{time}h.fastq #> source2: #> /path/from/collaborator/weirdNamingScheme_{external_id}.fastq #> name: example_derive diff --git a/articles/feature4_derivedImpliedAttributes.html b/articles/feature4_derivedImpliedAttributes.html index a7afb3e..fd46823 100644 --- a/articles/feature4_derivedImpliedAttributes.html +++ b/articles/feature4_derivedImpliedAttributes.html @@ -260,7 +260,7 @@

Code package = "pepr" ) p = Project(projectConfig) -## Loading config file: /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_derive_imply/project_config.yaml +## Loading config file: /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_derive_imply/project_config.yaml

And inspect it:

 sampleTable(p)
diff --git a/articles/feature5_sampleSubtable.html b/articles/feature5_sampleSubtable.html
index 93f377f..1f36581 100644
--- a/articles/feature5_sampleSubtable.html
+++ b/articles/feature5_sampleSubtable.html
@@ -275,7 +275,7 @@ 
Example 1: basic sample suba
 package = "pepr"
 )
 p1 = Project(projectConfig1)
-#> Loading config file: /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_subtable1/project_config.yaml
+#> Loading config file: /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_subtable1/project_config.yaml
 # Check the files
 p1Samples = sampleTable(p1)
 p1Samples$file
@@ -533,7 +533,7 @@ 
Example 2: subannotatio
 package = "pepr"
 )
 p2 = Project(projectConfig2)
-#> Loading config file: /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_subtable2/project_config.yaml
+#> Loading config file: /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_subtable2/project_config.yaml
 #> Warning in `[<-.data.frame`(x, i, j, value): replacement element 1 has 3 rows
 #> to replace 1 rows
 #> Warning in `[<-.data.frame`(x, i, j, value): replacement element 1 has 2 rows
@@ -773,7 +773,7 @@ 
Example 3: subannotat
 package = "pepr"
 )
 p3 = Project(projectConfig3)
-#> Loading config file: /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_subtable3/project_config.yaml
+#> Loading config file: /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_subtable3/project_config.yaml
 #> Warning in `[<-.data.frame`(x, i, j, value): replacement element 1 has 3 rows
 #> to replace 1 rows
 # Check the files
@@ -964,7 +964,7 @@ 
Example 4:
 package = "pepr"
 )
 p4 = Project(projectConfig4)
-#> Loading config file: /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_subtable4/project_config.yaml
+#> Loading config file: /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_subtable4/project_config.yaml
 # Check the read1 and read2 columns
 p4Samples = sampleTable(p4)
 p4Samples$read1
diff --git a/articles/feature6_amendments.html b/articles/feature6_amendments.html
index 02abac1..86d9ee4 100644
--- a/articles/feature6_amendments.html
+++ b/articles/feature6_amendments.html
@@ -437,7 +437,7 @@ 
Code
 
 projectConfig = system.file("extdata", paste0("example_peps-", branch),"example_amendments1", "project_config.yaml", package="pepr")
 p=Project(projectConfig)
-#> Loading config file: /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/project_config.yaml
+#> Loading config file: /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/project_config.yaml
 #>   amendments: newLib,newLib2

 
An appropriate message is displayed, which informs you what are the
 names of the amendments that you have defined in the
@@ -465,7 +465,7 @@ 
Code
 #>   amendments: newLib,newLib2
 pNewLib = Project(file = projectConfig, amendments = "newLib")
-#> Loading config file: /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/project_config.yaml
+#> Loading config file: /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/project_config.yaml
 #> Activating amendment: newLib
 #>   amendments: newLib,newLib2

Let’s inspect it:

@@ -500,8 +500,8 @@

Code #> Config object. Class: Config #> pep_version: 2.0.0 #> sample_table: -#> /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/sample_table.csv -#> output_dir: /Users/runner/hello_looper_results +#> /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/sample_table.csv +#> output_dir: /home/runner/hello_looper_results #> sample_modifiers: #> derive: #> attributes: file_path diff --git a/articles/gettingStarted.html b/articles/gettingStarted.html index 92ff5d9..0f2a85f 100644 --- a/articles/gettingStarted.html +++ b/articles/gettingStarted.html @@ -137,7 +137,7 @@

Loading an example projectLoading your project metadata into R is a single line of code:

 p = pepr::Project(file=projectConfigFile)
-
## Loading config file: /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_basic/project_config.yaml
+
## Loading config file: /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_basic/project_config.yaml

That’s it! You’ve now have a Project object, p, to interact with in R.

@@ -153,7 +153,7 @@

Interfacing with your p 
## PEP project object. Class:  Project
 ##   file:  
-## /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_basic/project_config.yaml
+## /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_basic/project_config.yaml
 ##   samples:  2

To get the sample table out of the project, you use the samples() function:

@@ -169,7 +169,7 @@

Interfacing with your ## Config object. Class: Config ## pep_version: 2.0.0 ## sample_table: -## /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_basic/sample_table.csv +## /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_basic/sample_table.csv ## name: example_basic

Follow the other vignettes for more advanced capabilities of pepr.

diff --git a/authors.html b/authors.html index 32aac7d..84291f4 100644 --- a/authors.html +++ b/authors.html @@ -71,11 +71,11 @@

Authors

  • -

    Nathan Sheffield. Author, copyright holder. +

    Nathan Sheffield. Author, copyright holder, maintainer.

  • -

    Michal Stolarczyk. Author, maintainer. +

    Michal Stolarczyk. Author.

diff --git a/index.html b/index.html index 81e9a4d..9fcd511 100644 --- a/index.html +++ b/index.html @@ -153,8 +153,8 @@

Citation

Developers

    -
  • Nathan Sheffield
    Author, copyright holder
    • -
  • Michal Stolarczyk
    Author, maintainer
    • +
  • Nathan Sheffield
    Author, copyright holder, maintainer
    • +
  • Michal Stolarczyk
    Author
diff --git a/pkgdown.yml b/pkgdown.yml index 9374a92..b3b30a3 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -9,5 +9,5 @@ articles: feature5_sampleSubtable: feature5_sampleSubtable.html feature6_amendments: feature6_amendments.html gettingStarted: gettingStarted.html -last_built: 2023-11-17T01:23Z +last_built: 2023-11-17T01:32Z diff --git a/reference/Config-class.html b/reference/Config-class.html index d302de5..45afdf8 100644 --- a/reference/Config-class.html +++ b/reference/Config-class.html @@ -100,7 +100,7 @@

Examples

projectConfig = system.file("extdata", "example_peps-master",
 "example_amendments1", "project_config.yaml", package="pepr")
 c=Config(projectConfig)
-#> Loading config file: /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/project_config.yaml
+#> Loading config file: /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/project_config.yaml
 #>   amendments: newLib,newLib2
diff --git a/reference/Project.html b/reference/Project.html index c1da046..6e0beff 100644 --- a/reference/Project.html +++ b/reference/Project.html @@ -109,7 +109,7 @@

Examples

projectConfig = system.file("extdata", "example_peps-master",
 "example_amendments1", "project_config.yaml", package="pepr")
 p=Project(projectConfig)
-#> Loading config file: /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/project_config.yaml
+#> Loading config file: /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/project_config.yaml
 #>   amendments: newLib,newLib2
diff --git a/reference/activateAmendments.html b/reference/activateAmendments.html index 7d4a9b1..a61b85f 100644 --- a/reference/activateAmendments.html +++ b/reference/activateAmendments.html @@ -113,7 +113,7 @@

Examples

"project_config.yaml", package = "pepr") p = Project(file = projectConfig) -#> Loading config file: /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/project_config.yaml +#> Loading config file: /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/project_config.yaml #> amendments: newLib,newLib2 availAmendments = listAmendments(p) #> amendments: newLib,newLib2 @@ -121,7 +121,7 @@

Examples

#> Activating amendment: newLib #> PEP project object. Class: Project #> file: -#> /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/project_config.yaml +#> /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/project_config.yaml #> samples: 4 #> amendments: newLib,newLib2 diff --git a/reference/checkSection.html b/reference/checkSection.html index f2011e7..a135d1b 100644 --- a/reference/checkSection.html +++ b/reference/checkSection.html @@ -115,7 +115,7 @@

Examples

projectConfig = system.file("extdata", "example_peps-master",
 "example_amendments1", "project_config.yaml", package="pepr")
 p=Project(projectConfig)
-#> Loading config file: /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/project_config.yaml
+#> Loading config file: /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/project_config.yaml
 #>   amendments: newLib,newLib2
 checkSection(config(p),sectionNames = c("amendments","newLib"))
 #> [1] FALSE
diff --git a/reference/config.html b/reference/config.html
index 637357b..c36664f 100644
--- a/reference/config.html
+++ b/reference/config.html
@@ -106,14 +106,14 @@ 
Examples

     
projectConfig = system.file("extdata", "example_peps-master",
 "example_amendments1", "project_config.yaml", package="pepr")
 p=Project(projectConfig)
-#> Loading config file: /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/project_config.yaml
+#> Loading config file: /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/project_config.yaml
 #>   amendments: newLib,newLib2
 config(p)
 #> Config object. Class: Config
 #>  pep_version: 2.0.0
 #>  sample_table: 
-#> /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/sample_table.csv
-#>  output_dir: /Users/runner/hello_looper_results
+#> /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/sample_table.csv
+#>  output_dir: /home/runner/hello_looper_results
 #>  sample_modifiers:
 #>     derive:
 #>         attributes: file_path
diff --git a/reference/dot-expandList.html b/reference/dot-expandList.html
index 2adaa03..ddafdf0 100644
--- a/reference/dot-expandList.html
+++ b/reference/dot-expandList.html
@@ -98,7 +98,7 @@ 
Examples

 #> $a
 #> $a$b
 #> $a$b$c
-#> [1] "/Users/runner/test.txt"
+#> [1] "/home/runner/test.txt"
 #> 
 #> 
 #> 
diff --git a/reference/dot-expandPath.html b/reference/dot-expandPath.html
index 3e127e8..71e73b6 100644
--- a/reference/dot-expandPath.html
+++ b/reference/dot-expandPath.html
@@ -107,7 +107,7 @@ 
Examples

 #> [1] "https://www.r-project.org/"
 path = "$HOME/my/path/string.txt"
 .expandPath(path)
-#> [1] "/Users/runner/my/path/string.txt"
+#> [1] "/home/runner/my/path/string.txt"
diff --git a/reference/dot-printNestedList.html b/reference/dot-printNestedList.html index 0ca1b83..2b80f58 100644 --- a/reference/dot-printNestedList.html +++ b/reference/dot-printNestedList.html @@ -101,11 +101,11 @@

Examples

"project_config.yaml", package = "pepr") p = Project(file = projectConfig) -#> Loading config file: /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_basic/project_config.yaml +#> Loading config file: /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_basic/project_config.yaml .printNestedList(config(p),level=2) #> pep_version: 2.0.0 #> sample_table: -#> /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_basic/sample_table.csv +#> /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_basic/sample_table.csv #> name: example_basic diff --git a/reference/dot-strformat.html b/reference/dot-strformat.html index ac77068..3719457 100644 --- a/reference/dot-strformat.html +++ b/reference/dot-strformat.html @@ -104,9 +104,9 @@

Arguments

Examples

.strformat("~/{VAR1}{VAR2}_file", list(VAR1="hi", VAR2="hello"))
-#> [1] "/Users/runner/hihello_file"
+#> [1] "/home/runner/hihello_file"
 .strformat("$HOME/{VAR1}{VAR2}_file", list(VAR1="hi", VAR2="hello"))
-#> [1] "/Users/runner/hihello_file"
+#> [1] "/home/runner/hihello_file"
diff --git a/reference/fetchSamples.html b/reference/fetchSamples.html index ce7dffe..d7efb9d 100644 --- a/reference/fetchSamples.html +++ b/reference/fetchSamples.html @@ -112,7 +112,7 @@

Examples

projectConfig = system.file("extdata", "example_peps-master",
 "example_amendments1", "project_config.yaml", package="pepr")
 p = Project(projectConfig)
-#> Loading config file: /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/project_config.yaml
+#> Loading config file: /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/project_config.yaml
 #>   amendments: newLib,newLib2
 s = sampleTable(p)
 fetchSamples(s,attr = "sample_name", func=function(x){ which(x=="pig_0h") },action="include")
diff --git a/reference/getSample.html b/reference/getSample.html
index 8eb7247..1dcc0d2 100644
--- a/reference/getSample.html
+++ b/reference/getSample.html
@@ -113,7 +113,7 @@ 
Examples

 package = "pepr"
 )
 p = Project(projectConfig)
-#> Loading config file: /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_basic/project_config.yaml
+#> Loading config file: /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_basic/project_config.yaml
 sampleName = "frog_1"
 getSample(p, sampleName)
 #>    sample_name      protocol                file
diff --git a/reference/getSubsample.html b/reference/getSubsample.html
index 06dbbe0..abfe6f1 100644
--- a/reference/getSubsample.html
+++ b/reference/getSubsample.html
@@ -121,7 +121,7 @@ 
Examples

 package = "pepr"
 )
 p = Project(projectConfig)
-#> Loading config file: /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_subtable1/project_config.yaml
+#> Loading config file: /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_subtable1/project_config.yaml
 sampleName = "frog_1"
 subsampleName = "sub_a"
 getSubsample(p, sampleName, subsampleName)
diff --git a/reference/listAmendments.html b/reference/listAmendments.html
index 60a47b8..32d5b2a 100644
--- a/reference/listAmendments.html
+++ b/reference/listAmendments.html
@@ -111,7 +111,7 @@ 
Examples

 "project_config.yaml",
 package = "pepr")
 p = Project(file = projectConfig)
-#> Loading config file: /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/project_config.yaml
+#> Loading config file: /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/project_config.yaml
 #>   amendments: newLib,newLib2
 availAmendemtns = listAmendments(p)
 #>   amendments: newLib,newLib2
diff --git a/reference/sampleTable.html b/reference/sampleTable.html
index 28c6df3..05bb01f 100644
--- a/reference/sampleTable.html
+++ b/reference/sampleTable.html
@@ -106,7 +106,7 @@ 
Examples

     
projectConfig = system.file("extdata", "example_peps-master",
 "example_amendments1", "project_config.yaml", package="pepr")
 p=Project(projectConfig)
-#> Loading config file: /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/project_config.yaml
+#> Loading config file: /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/project_config.yaml
 #>   amendments: newLib,newLib2
 sampleTable(p)
 #>    sample_name protocol organism time                       file_path
diff --git a/reference/select-config.html b/reference/select-config.html
index 8c04ff2..a3eba76 100644
--- a/reference/select-config.html
+++ b/reference/select-config.html
@@ -115,18 +115,18 @@ 
Examples

     
projectConfig = system.file("extdata", "example_peps-master",
 "example_amendments1", "project_config.yaml", package="pepr")
 c=Config(projectConfig)
-#> Loading config file: /Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/project_config.yaml
+#> Loading config file: /home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/project_config.yaml
 #>   amendments: newLib,newLib2
 c[[2]]
-#> [1] "/Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/sample_table.csv"
+#> [1] "/home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/sample_table.csv"
 c[2]
 #> [[1]]
-#> [1] "/Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/sample_table.csv"
+#> [1] "/home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/sample_table.csv"
 #> 
 c[["sample_table"]]
-#> [1] "/Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/sample_table.csv"
+#> [1] "/home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/sample_table.csv"
 c$sample_table
-#> [1] "/Users/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/sample_table.csv"
+#> [1] "/home/runner/work/_temp/Library/pepr/extdata/example_peps-master/example_amendments1/sample_table.csv"