fix: SAMPLES -> samples

Author: cmeesters

setup_creators/solutions/06_Snakefile_run

@@ -1,5 +1,5 @@
 # our samples are pre-configured
-SAMPLES = ["A", "B"]
+samples = ["A", "B"]
 
 rule all:
     input:
@@ -38,8 +38,8 @@ rule samtools_index:
 rule bcftools_call:
     input:
         fa="data/genome.fa",
-        bam=expand("sorted_reads/{sample}.bam", sample=SAMPLES),
-        bai=expand("sorted_reads/{sample}.bam.bai", sample=SAMPLES)
+        bam=expand("sorted_reads/{sample}.bam", sample=samples),
+        bai=expand("sorted_reads/{sample}.bam.bai", sample=samples)
     output:
         "calls/all.vcf"
     shell:

setup_creators/solutions/07_Snakefile_script

@@ -1,5 +1,5 @@
 # our samples are pre-configured
-SAMPLES = ["A", "B"]
+samples = ["A", "B"]
 
 
 rule all:
@@ -40,8 +40,8 @@ rule samtools_index:
 rule bcftools_call:
     input:
         fa="data/genome.fa",
-        bam=expand("sorted_reads/{sample}.bam", sample=SAMPLES),
-        bai=expand("sorted_reads/{sample}.bam.bai", sample=SAMPLES)
+        bam=expand("sorted_reads/{sample}.bam", sample=samples),
+        bai=expand("sorted_reads/{sample}.bam.bai", sample=samples)
     output:
         "calls/all.vcf"
     shell:

setup_creators/solutions/08_Snakefile_script2

@@ -1,5 +1,5 @@
 # our samples are pre-configured
-SAMPLES = ["A", "B"]
+samples = ["A", "B"]
 
 configfile: "config/config.yaml"
 
@@ -41,8 +41,8 @@ rule samtools_index:
 rule bcftools_call:
     input:
         fa="data/genome.fa",
-        bam=expand("sorted_reads/{sample}.bam", sample=SAMPLES),
-        bai=expand("sorted_reads/{sample}.bam.bai", sample=SAMPLES)
+        bam=expand("sorted_reads/{sample}.bam", sample=samples),
+        bai=expand("sorted_reads/{sample}.bam.bai", sample=samples)
     output:
         "calls/all.vcf"
     shell:

setup_creators/solutions/09_Snakefile_config

@@ -1,5 +1,5 @@
 # our samples are pre-configured
-SAMPLES = ["A", "B"]
+samples = ["A", "B"]
 
 configfile: "config/config.yaml"
 
@@ -41,8 +41,8 @@ rule samtools_index:
 rule bcftools_call:
     input:
         fa="data/genome.fa",
-        bam=expand("sorted_reads/{sample}.bam", sample=SAMPLES),
-        bai=expand("sorted_reads/{sample}.bam.bai", sample=SAMPLES)
+        bam=expand("sorted_reads/{sample}.bam", sample=samples),
+        bai=expand("sorted_reads/{sample}.bam.bai", sample=samples)
     output:
         "calls/all.vcf"
     shell:

setup_creators/tutorial/05_Snakefile_target

@@ -1,5 +1,5 @@
 # our samples are pre-configured
-SAMPLES = ["A", "B"]
+samples = ["A", "B"]
 
 #TASK: Figure out, which your final target is.
 #      This is the final target of our workflow, so far.
@@ -44,8 +44,8 @@ rule samtools_index:
 rule bcftools_call:
     input:
         fa="data/genome.fa",
-        bam=expand("sorted_reads/{sample}.bam", sample=SAMPLES),
-        bai=expand("sorted_reads/{sample}.bam.bai", sample=SAMPLES)
+        bam=expand("sorted_reads/{sample}.bam", sample=samples),
+        bai=expand("sorted_reads/{sample}.bam.bai", sample=samples)
     output:
         "calls/all.vcf"
     shell:

setup_creators/tutorial/06_Snakefile_run

@@ -1,5 +1,5 @@
 # our samples are pre-configured
-SAMPLES = ["A", "B"]
+samples = ["A", "B"]
 
 #TASKS: This is an almost working Snakefile!
 #       But it is scrambled and contains a bug. 
@@ -36,8 +36,8 @@ rule samtools_sort:
 rule bcftools_call:
     input:
         fa="data/genome.fa",
-        bam=expand("sorted_reads/{sample}.bam", sample=SAMPLES),
-        bai=expand("sorted_reads/{sample}.bam.bai", sample=SAMPLES)
+        bam=expand("sorted_reads/{sample}.bam", sample=samples),
+        bai=expand("sorted_reads/{sample}.bam.bai", sample=samples)
     output:
         "calls/all.vcf"
     shell: