From a7e5b632c73e5d321a3a46fc6d10251c5b6aee94 Mon Sep 17 00:00:00 2001
From: Thiseas Lamnidis <thisseass@gmail.com>
Date: Fri, 2 Feb 2024 12:23:14 +0000
Subject: [PATCH] ignore dev_docs.md when linting. fix indent

---
 .prettierignore              |  1 +
 docs/development/dev_docs.md | 28 ++++++++++++++--------------
 2 files changed, 15 insertions(+), 14 deletions(-)

diff --git a/.prettierignore b/.prettierignore
index 6f762db0b..30f2a16d8 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -12,3 +12,4 @@ testing*
 bin/
 *.cff
 test/
+dev_docs.md
diff --git a/docs/development/dev_docs.md b/docs/development/dev_docs.md
index 13b1b9d72..e7c0a0f57 100644
--- a/docs/development/dev_docs.md
+++ b/docs/development/dev_docs.md
@@ -9,26 +9,26 @@ To add new input files or options to the reference sheet, you have to complete a
 1. Add your new parameter to nextflow.config.
 2. Add parameter description to schema (nf-core schema build).
 3. Read in new parameter (params.<NEW>) as input within the reference_indexing_single local subworkflow.
-  1. Add new line to the large `.map{}` operation starting on [line 80(https://github.com/nf-core/eager/blob/d4211582f349cc30c88202c12942218f99006041/subworkflows/local/reference_indexing_single.nf#L80)] and add check if the file exists. `def <PARAM_NAME> = params.<NEW> != null ? file(params.<NEW>, checkIfExists: true ) : ""`
-  2. Add <PARAM_NAME> to the result of the map operation. Double-check the order!
-  3. With the `ch_ref_index_single.multiMap{}` below you add the reference name as a meta. You can also combine your new parameter with others if useful for the workflow step. `<NEW_SUBCHANNE>: [ meta, <PARAM_NAME> ]`
-  4. Add your ch_ref_index_single.<NEW_SUBCHANNEL> to the final emit. `<NEW_EMIT> = ch_ref_index_single.<NEW_SUBCHANNEL>`
+    1. Add new line to the large `.map{}` operation starting on [line 80](https://github.com/nf-core/eager/blob/d4211582f349cc30c88202c12942218f99006041/subworkflows/local/reference_indexing_single.nf#L80) and add check if the file exists. `def <PARAM_NAME> = params.<NEW> != null ? file(params.<NEW>, checkIfExists: true ) : ""`
+    2. Add <PARAM_NAME> to the result of the map operation. Double-check the order!
+    3. With the `ch_ref_index_single.multiMap{}` below you add the reference name as a meta. You can also combine your new parameter with others if useful for the workflow step. `<NEW_SUBCHANNE>: [ meta, <PARAM_NAME> ]`
+    4. Add your ch_ref_index_single.<NEW_SUBCHANNEL> to the final emit. `<NEW_EMIT> = ch_ref_index_single.<NEW_SUBCHANNEL>`
 
 ### Multi-reference input workflow
 
 1. Add new column named <SOFTWARE_FILETYPE> and test data to the test reference sheet (https://github.com/nf-core/test-datasets/blob/eager/reference/reference_sheet_multiref.csv).
 2. Read in new input within the reference_indexing_multi local subworkflow.
-  1. Add new line to the large `.map{}` operation starting on [line 30](https://github.com/nf-core/eager/blob/d4211582f349cc30c88202c12942218f99006041/subworkflows/local/reference_indexing_multi.nf#L30). Add check if the file exists if appropriate. `def <PARAM_NAME> = row["<SOFTWARE_FILETYPE>"] != "" ? file(row["<SOFTWARE_FILETYPE>"], checkIfExists: true) : ""`
-  2. Add <PARAM_NAME> to the result of the `.map{}` operation. Double-check the order!
-  3. With the `ch_input_from_referencesheet.multiMap{}` below you add the reference name as a meta. You can also combine your new parameter with others if useful for the workflow step. `<NEW_SUBCHANNEL>: [ meta, <PARAM_NAME> ]`
-  4. Add ch_input_from_referencesheet.<NEW_SUBCHANNEL> to the final emit. `<NEW_EMIT> = ch_input_from_referencesheet.<NEW_SUBCHANNEL>`
+    1. Add new line to the large `.map{}` operation starting on [line 30](https://github.com/nf-core/eager/blob/d4211582f349cc30c88202c12942218f99006041/subworkflows/local/reference_indexing_multi.nf#L30). Add check if the file exists if appropriate. `def <PARAM_NAME> = row["<SOFTWARE_FILETYPE>"] != "" ? file(row["<SOFTWARE_FILETYPE>"], checkIfExists: true) : ""`
+    2. Add <PARAM_NAME> to the result of the `.map{}` operation. Double-check the order!
+    3. With the `ch_input_from_referencesheet.multiMap{}` below you add the reference name as a meta. You can also combine your new parameter with others if useful for the workflow step. `<NEW_SUBCHANNEL>: [ meta, <PARAM_NAME> ]`
+    4. Add ch_input_from_referencesheet.<NEW_SUBCHANNEL> to the final emit. `<NEW_EMIT> = ch_input_from_referencesheet.<NEW_SUBCHANNEL>`
 
 ### Combining in the Reference Indexing workflow
 
 1. Add you new parameter channel to the `if` condition selecting between the direct parameter input or the reference sheet input.
-  1. below "REFERENCE_INDEXING_MULTI" for reference sheet input `<NEW_CHANNEL> = REFERENCE_INDEXING_MULTI.out.<NEW_EMIT>`
-  2. below "REFERENCE_INDEXING_SINGLE" `<NEW_CHANNEL> = REFERENCE_INDEXING_SINGLE.out.<NEW_EMIT>`
-  3. Filter out options that have not been provided. `<NEW_CHANNEL> = <NEW_CHANNEL>.filter{ it[1] != "" }`
-  4. Add unzipping of zipped input files with GUNZIP.
-  5. Add <NEW_CHANNEL> to the final emit. `<NEW_EMIT> = <NEW_CHANNEL>`
-  6. Call new inputs within the main eager.nf with `REFERENCE_INDEXING.out.<NEW_EMIT>`.
+    1. below "REFERENCE_INDEXING_MULTI" for reference sheet input `<NEW_CHANNEL> = REFERENCE_INDEXING_MULTI.out.<NEW_EMIT>`
+    2. below "REFERENCE_INDEXING_SINGLE" `<NEW_CHANNEL> = REFERENCE_INDEXING_SINGLE.out.<NEW_EMIT>`
+    3. Filter out options that have not been provided. `<NEW_CHANNEL> = <NEW_CHANNEL>.filter{ it[1] != "" }`
+    4. Add unzipping of zipped input files with GUNZIP.
+    5. Add <NEW_CHANNEL> to the final emit. `<NEW_EMIT> = <NEW_CHANNEL>`
+    6. Call new inputs within the main eager.nf with `REFERENCE_INDEXING.out.<NEW_EMIT>`.