Validate other yaml files

Makefile

@@ -115,8 +115,8 @@ check-slides: build  ## check the markdown-formatted links in slides
 
 check-yaml: ## lint yaml files
 	( $(ACTIVATE_ENV) && \
-	  find . -path "**/*.yaml" | xargs -L 1 -I '{}' sh -c "yamllint {}" \
-	  find . -path "**/*.yml" | xargs -L 1 -I '{}' sh -c "yamllint {}" \
+	  find . -name "*.yaml" | xargs -L 1 -I '{}' sh -c "yamllint {}" \
+	  find topics -name '*.yml' | xargs -L 1 -I '{}' sh -c "yamllint {}" \
 	)
 .PHONY: check-yaml
 

topics/assembly/tutorials/general-introduction/workflows/assembly-general-introduction-job.yml

@@ -1,3 +1,4 @@
+---
 mutant_R1.fastq:
   class: File
   location: https://zenodo.org/record/582600/files/mutant_R1.fastq

topics/assembly/tutorials/general-introduction/workflows/assembly-general-introduction-test.yml

@@ -1,11 +1,11 @@
+---
 - doc: Test sample data for the unicycler assembly workflow
   job: assembly-general-introduction-job.yml
   outputs:
     fasta_stats_tabular:
-      asserts:
-        has_n_columns:
-          n: 2
+      #asserts:
+        #has_n_columns:
+          #n: 2
       asserts:
         has_line:
           line: 'GC_content	33.6'
-

topics/assembly/tutorials/unicycler-assembly/workflows/unicycler-job.yml

@@ -1,3 +1,4 @@
+---
 forward_reads:
   # https://zenodo.org/record/940733/files/illumina_f.fq
   class: File

topics/assembly/tutorials/unicycler-assembly/workflows/unicycler-test.yml

@@ -1,3 +1,4 @@
+---
 - doc: Test sample data for the unicycler assembly workflow
   job: unicycler-job.yml
   outputs:
@@ -11,5 +12,5 @@
           line: '     CDS             70..1404'
     tbl:
       asserts:
-        has_text:          
+        has_text:
           line: '			product	DNA polymerase III, holoenzyme'

topics/chip-seq/tutorials/formation_of_super-structures_on_xi/workflows/formation_of_super_structures_on_xi-job.yml

@@ -1,3 +1,4 @@
+---
 wt_H3K4me3_read1:
   class: File
   location: https://zenodo.org/record/1324070/files/wt_H3K4me3_read1.fastq.gz
@@ -27,4 +28,4 @@ wt_input_rep1:
   location: https://zenodo.org/record/1324070/files/wt_input_rep1.fastq.gz
 wt_input_rep2:
   class: File
-  location: https://zenodo.org/record/1324070/files/wt_input_rep2.fastq.gz
+  location: https://zenodo.org/record/1324070/files/wt_input_rep2.fastq.gz

topics/chip-seq/tutorials/formation_of_super-structures_on_xi/workflows/formation_of_super_structures_on_xi-test.yml

@@ -1,4 +1,5 @@
-doc: Test sample data for ChIP-seq:formation_of_super_structures_on_xi
+---
+- doc: "Test sample data for ChIP-seq:formation_of_super_structures_on_xi"
   job: formation_of_super_structures_on_xi-job.yml
   outputs:
     wt_H3K4me3_rep1_read1_fastqc:
@@ -13,10 +14,6 @@ doc: Test sample data for ChIP-seq:formation_of_super_structures_on_xi
       asserts:
         has_text:
           text: '1569 (3.14%)'
-    wt_H3K4me3_rep1_trim_galore:
-      asserts:
-        has_text:
-          text: '1569 (3.14%)'
     wt_H3K4me3_rep1_bowtie2:
       asserts:
         has_text:
@@ -44,4 +41,4 @@ doc: Test sample data for ChIP-seq:formation_of_super_structures_on_xi
     wt_all_mergebed:
       asserts:
         has_text:
-          text: '3402493'
+          text: '3402493'

topics/epigenetics/tutorials/methylation-seq/workflows/methylation-seq-job.yml

@@ -1,3 +1,4 @@
+---
 subset_1.fastq:
   class: File
   location: https://zenodo.org/record/557099/files/subset_1.fastq
@@ -25,4 +26,3 @@ BT126_CpG.meth.bedGraph:
 BT198_CpG.meth.bedGraph:
   class: File
   location: https://zenodo.org/record/557099/files/BT198_CpG.meth.bedGraph
-

topics/epigenetics/tutorials/methylation-seq/workflows/methylation-seq-test.yml

@@ -1,3 +1,4 @@
+---
 - doc: Test sample data for the unicycler assembly workflow
   job: methylation-seq-job.yml
   outputs:

topics/metagenomics/tutorials/general-tutorial/workflows/amplicon-job.yml

@@ -1,3 +1,4 @@
+---
 silva:
   class: File
   location: https://zenodo.org/record/815875/files/silva.v4.fasta

topics/metagenomics/tutorials/general-tutorial/workflows/amplicon-test.yml

@@ -1,8 +1,8 @@
+---
 - doc: Test sample data for the amplicon tutorial
   job: amplicon-job.yml
   outputs:
     mothur_make_shared_shared:
-      asserts:
       asserts:
         has_text:
           text: "0.03	anguil	4015	250	145	167	181	122"

topics/sequence-analysis/tutorials/mapping/workflows/mapping-job.yml

@@ -1,6 +1,7 @@
+---
 reads_1:
   class: File
   location: https://zenodo.org/record/1324070/files/wt_H3K4me3_read1.fastq.gz
 reads_2:
   class: File
-  location: https://zenodo.org/record/1324070/files/wt_H3K4me3_read1.fastq.gz
+  location: https://zenodo.org/record/1324070/files/wt_H3K4me3_read1.fastq.gz

topics/sequence-analysis/tutorials/mapping/workflows/mapping-test.yml

@@ -1,4 +1,5 @@
-doc: Test sample data for Sequence analysis:Mapping
+---
+- doc: "Test sample data for Sequence analysis:Mapping"
   job: mapping-job.yml
   outputs:
     bowtie2_mapping_stats:
@@ -12,4 +13,4 @@ doc: Test sample data for Sequence analysis:Mapping
     bam_stats_2:
       asserts:
         has_text:
-          text: '4466767'
+          text: '4466767'

topics/sequence-analysis/tutorials/quality-control/workflows/quality_control-job.yml

@@ -1,6 +1,7 @@
+---
 reads_1:
   class: File
   location: https://zenodo.org/record/61771/files/GSM461178_untreat_paired_subset_1.fastq
 reads_2:
   class: File
-  location: https://zenodo.org/record/61771/files/GSM461178_untreat_paired_subset_2.fastq
+  location: https://zenodo.org/record/61771/files/GSM461178_untreat_paired_subset_2.fastq

topics/sequence-analysis/tutorials/quality-control/workflows/quality_control-test.yml

@@ -1,23 +1,24 @@
-doc: Test sample data for Sequence-analyses:Quality-control
+---
+- doc: "Test sample data for Sequence-analyses:Quality-control"
   job: quality_control-job.yml
   outputs:
     reads_1_fastqc:
       asserts:
         has_text:
-            text: 'Sanger / Illumina 1.9'
+          text: 'Sanger / Illumina 1.9'
     reads_1_cutadapt:
       asserts:
         has_text:
-            text: '3,651,491 bp (98.7%)'
+          text: '3,651,491 bp (98.7%)'
     reads_2_fastqc:
       asserts:
         has_text:
-            text: 'Sequence length	37'
+          text: 'Sequence length	37'
     reads_cutadapt:
       asserts:
         has_text:
-            text: '98,624 (98.6%)'
+          text: '98,624 (98.6%)'
     multiqc:
       asserts:
         has_text:
-            text: 'FastQC'
+          text: 'FastQC'

topics/transcriptomics/tutorials/ref-based/workflows/ref_based-job.yml

@@ -1,3 +1,4 @@
+---
 GSM461177_1:
   class: File
   location: https://zenodo.org/record/1185122/files/GSM461177_1.fastqsanger
@@ -33,4 +34,4 @@ GSM461181_treat_paired.counts:
   location: https://zenodo.org/record/1185122/files/GSM461181_treat_paired.counts
 GSM461182_untreat_single.counts:
   class: File
-  location: https://zenodo.org/record/1185122/files/GSM461182_untreat_single.counts
+  location: https://zenodo.org/record/1185122/files/GSM461182_untreat_single.counts

topics/transcriptomics/tutorials/ref-based/workflows/ref_based-test.yml

@@ -1,4 +1,5 @@
-doc: Test sample data for Transcriptomics:Refence-based
+---
+- doc: "Test sample data for Transcriptomics:Refence-based"
   job: ref_based-job.yml
   outputs:
     GSM461177_1_fastqc:
@@ -45,6 +46,3 @@ doc: Test sample data for Transcriptomics:Refence-based
       asserts:
         has_text:
           text: 'GO:0005576'
-
-
-

topics/variant-analysis/tutorials/microbial-variants/workflows/microbial_variant_calling-job.yml

@@ -1,3 +1,4 @@
+---
 mutant_R1:
   class: File
   location: https://zenodo.org/record/582600/files/mutant_R1.fastq

topics/variant-analysis/tutorials/microbial-variants/workflows/microbial_variant_calling-test.yml

@@ -1,3 +1,4 @@
+---
 - doc: Test sample data for Microbial variant calling workflow
   job: microbial_variant_calling-job.yml
   outputs: