From d1fc03e75f81b469457a97dc22353df44d708e91 Mon Sep 17 00:00:00 2001
From: magdalenazz <magdalenazz477@gmail.com>
Date: Wed, 19 Jun 2024 16:42:28 +0200
Subject: [PATCH] fix: linting

---
 docs/softwares.md                  | 2 +-
 workflow/Snakefile                 | 2 +-
 workflow/rules/longqc.smk          | 2 +-
 workflow/schemas/rules.schema.yaml | 6 +++---
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/docs/softwares.md b/docs/softwares.md
index 43d5c95..574ce87 100644
--- a/docs/softwares.md
+++ b/docs/softwares.md
@@ -69,7 +69,7 @@ Calculate coverage in specified regions that is used by gatk_calculate_contamina
 
 ---
 
-## [longqc_sampleqc](url_to_tool)
+## [longqc_sampleqc](https://github.com/yfukasawa/LongQC)
 Introduction to longqc_sampleqc
 
 ### :snake: Rule
diff --git a/workflow/Snakefile b/workflow/Snakefile
index 55bdf7d..7080b79 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -5,7 +5,7 @@ __license__ = "GPL-3"
 
 
 include: "rules/common.smk"
-include: "rules/longqc.smk"
+#include: "rules/longqc.smk" not finished rule
 include: "rules/fastqc.smk"
 include: "rules/gatk.smk"
 include: "rules/mosdepth.smk"
diff --git a/workflow/rules/longqc.smk b/workflow/rules/longqc.smk
index e48ee62..1f5be9f 100644
--- a/workflow/rules/longqc.smk
+++ b/workflow/rules/longqc.smk
@@ -12,7 +12,7 @@ rule longqc_sampleqc:
     params:
         extra="--min_length 1000 --max_length 15000"  # example of additional parameters
     log:
-        "logs/longqc/sample_qc.log"
+        "qc/longqc_sampleqc/{sample}_{type}.sample_qc.log"
     benchmark:
         repeat(
             "qc/longqc_sampleqc/{sample}_{type}.output.benchmark.tsv",
diff --git a/workflow/schemas/rules.schema.yaml b/workflow/schemas/rules.schema.yaml
index 96e17b2..66b64ed 100644
--- a/workflow/schemas/rules.schema.yaml
+++ b/workflow/schemas/rules.schema.yaml
@@ -82,14 +82,14 @@ properties:
         type: object
         description: list of inputs
         properties:
-          input1:
+          fastq:
             type: string
-            description: Fastq filer med longread sekvenser
+            description: Fastq fil eller filer med longread sekvenser
       output:
         type: object
         description: list of outputs
         properties:
-          output1:
+          dir:
             type: string
             description: A folder with a collection of output files