Change path to tests

tests/software/bowtie2/align/test.yml

@@ -1,5 +1,5 @@
 - name: bowtie2 align single-end
-  command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_align_single_end -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/bowtie2/align -entry test_bowtie2_align_single_end -c tests/config/nextflow.config
   tags:
     - bowtie2
     - bowtie2_align_single_end
@@ -22,7 +22,7 @@
       should_exist: true
 
 - name: bowtie2 align paired-end
-  command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/bowtie2/align -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config
   tags:
     - bowtie2
     - bowtie2_align_paired_end

tests/software/bowtie2/build/test.yml

@@ -1,5 +1,5 @@
 - name: bowtie2 build
-  command: nextflow run ./tests/software/bowtie2 -entry test_bowtie2_build -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/bowtie2/build -entry test_bowtie2_build -c tests/config/nextflow.config
   tags:
     - bowtie2
     - bowtie2_build

tests/software/bwa/index/test.yml

@@ -1,5 +1,5 @@
 - name: bwa index
-  command: nextflow run ./tests/software/bwa -entry test_bwa_index -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/bwa/index -entry test_bwa_index -c tests/config/nextflow.config
   tags:
     - bwa
     - bwa_index

tests/software/bwa/mem/test.yml

@@ -1,5 +1,5 @@
 - name: bwa mem single-end
-  command: nextflow run ./tests/software/bwa -entry test_bwa_mem_single_end -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/bwa/mem -entry test_bwa_mem_single_end -c tests/config/nextflow.config
   tags:
     - bwa
     - bwa_mem
@@ -9,7 +9,7 @@
       md5sum: 3ee21210bac387e0335008146e4728bc
 
 - name: bwa mem paired-end
-  command: nextflow run ./tests/software/bwa -entry test_bwa_mem_paired_end -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/bwa/mem -entry test_bwa_mem_paired_end -c tests/config/nextflow.config
   tags:
     - bwa
     - bwa_mem

tests/software/dsh/filterbed/test.yml

@@ -1,5 +1,5 @@
 - name: dsh filterbed
-  command: nextflow run ./tests/software/dsh -entry test_dsh_filterbed -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/dsh/filterbed -entry test_dsh_filterbed -c tests/config/nextflow.config
   tags:
     - dsh
     - dsh_filterbed

tests/software/dsh/splitbed/test.yml

@@ -1,5 +1,5 @@
 - name: dsh splitbed
-  command: nextflow run ./tests/software/dsh -entry test_dsh_splitbed -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/dsh/splitbed -entry test_dsh_splitbed -c tests/config/nextflow.config
   tags:
     - dsh
     - dsh_splitbed

tests/software/picard/collectmultiplemetrics/test.yml

@@ -1,5 +1,5 @@
 - name: picard collectmultiplemetrics
-  command: nextflow run ./tests/software/picard -entry test_picard_collectmultiplemetrics -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics -c tests/config/nextflow.config
   tags:
     - picard
     - picard_collectmultiplemetrics

tests/software/picard/markduplicates/test.yml

@@ -1,5 +1,5 @@
 - name: picard markduplicates on sorted bam
-  command: nextflow run ./tests/software/picard -entry test_picard_markduplicates_sorted_bam -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/picard/markduplicates -entry test_picard_markduplicates_sorted_bam -c tests/config/nextflow.config
   tags:
     - picard
     - picard_markduplicates
@@ -9,7 +9,7 @@
       md5sum: 0ed0bfc94069380334ccd595f6d8207c
 
 - name: picard markduplicates on unsorted bam
-  command: nextflow run ./tests/software/picard -entry test_picard_markduplicates_unsorted_bam -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/picard/markduplicates -entry test_picard_markduplicates_unsorted_bam -c tests/config/nextflow.config
   tags:
     - picard
     - picard_markduplicates

tests/software/picard/mergesamfiles/test.yml

@@ -1,5 +1,5 @@
 - name: picard mergesamfiles
-  command: nextflow run ./tests/software/picard -entry test_picard_mergesamfiles -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/picard/mergesamfiles -entry test_picard_mergesamfiles -c tests/config/nextflow.config
   tags:
     - picard
     - picard_mergesamfiles

tests/software/preseq/lcextrap/test.yml

@@ -1,5 +1,5 @@
 - name: preseq lcextrap single-end
-  command: nextflow run ./tests/software/preseq -entry test_preseq_single_end -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/preseq/lcextrap -entry test_preseq_single_end -c tests/config/nextflow.config
   tags:
     - preseq
     - preseq_lcextrap
@@ -10,7 +10,7 @@
     - path: output/test_preseq_single_end/test.command.log
 
 - name: preseq lcextrap paired-end
-  command: nextflow run ./tests/software/preseq -entry test_preseq_paired_end -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/preseq/lcextrap -entry test_preseq_paired_end -c tests/config/nextflow.config
   tags:
     - preseq
     - preseq_lcextrap

tests/software/salmon/index/test.yml

@@ -1,5 +1,5 @@
 - name: salmon index
-  command: nextflow run ./tests/software/salmon -entry test_salmon_index -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/salmon/index -entry test_salmon_index -c tests/config/nextflow.config
   tags:
     - salmon
     - salmon_index

tests/software/salmon/quant/test.yml

@@ -1,5 +1,5 @@
 - name: salmon quant single-end
-  command: nextflow run ./tests/software/salmon -entry test_salmon_quant_single_end -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/salmon/quant -entry test_salmon_quant_single_end -c tests/config/nextflow.config
   tags:
     - salmon
     - salmon_quant

tests/software/samtools/flagstat/test.yml

@@ -1,5 +1,5 @@
 - name: samtools flagstat
-  command: nextflow run ./tests/software/samtools/ -entry test_samtools_flagstat -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/samtools/flagstat -entry test_samtools_flagstat -c tests/config/nextflow.config
   tags:
     - samtools
     - samtools_flagstat

tests/software/samtools/idxstats/test.yml

@@ -1,5 +1,5 @@
 - name: samtools idxstats
-  command: nextflow run ./tests/software/samtools/ -entry test_samtools_idxstats -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/samtools/idxstats -entry test_samtools_idxstats -c tests/config/nextflow.config
   tags:
     - samtools
     - samtools_idxstats

tests/software/samtools/index/test.yml

@@ -1,5 +1,5 @@
 - name: samtools index
-  command: nextflow run ./tests/software/samtools/ -entry test_samtools_index -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/samtools/index -entry test_samtools_index -c tests/config/nextflow.config
   tags:
     - samtools
     - samtools_index

tests/software/samtools/mpileup/test.yml

@@ -1,5 +1,5 @@
 - name: samtools mpileup
-  command: nextflow run ./tests/software/samtools/ -entry test_samtools_mpileup -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/samtools/mpileup -entry test_samtools_mpileup -c tests/config/nextflow.config
   tags:
     - samtools
     - samtools_mpileup

tests/software/samtools/sort/test.yml

@@ -1,5 +1,5 @@
 - name: samtools sort
-  command: nextflow run ./tests/software/samtools/ -entry test_samtools_sort -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/samtools/sort -entry test_samtools_sort -c tests/config/nextflow.config
   tags:
     - samtools
     - samtools_sort

tests/software/samtools/stats/test.yml

@@ -1,5 +1,5 @@
 - name: samtools stats
-  command: nextflow run ./tests/software/samtools/ -entry test_samtools_stats -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/samtools/stats -entry test_samtools_stats -c tests/config/nextflow.config
   tags:
     - samtools
     - samtools_stats

tests/software/samtools/view/test.yml

@@ -1,5 +1,5 @@
 - name: samtools view
-  command: nextflow run ./tests/software/samtools/ -entry test_samtools_view -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/samtools/view -entry test_samtools_view -c tests/config/nextflow.config
   tags:
     - samtools
     - samtools_view

tests/software/seacr/callpeak/test.yml

@@ -1,5 +1,5 @@
 - name: seacr callpeak
-  command: nextflow run ./tests/software/seacr/ -entry test_seacr_callpeak -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/seacr/callpeak -entry test_seacr_callpeak -c tests/config/nextflow.config
   tags:
     - seacr
     - seacr_callpeak

tests/software/star/align/test.yml

@@ -1,5 +1,5 @@
 - name: star align single-end
-  command: nextflow run ./tests/software/star -entry test_star_alignment_single_end -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/star/align -entry test_star_alignment_single_end -c tests/config/nextflow.config
   tags:
     - star
     - star_align
@@ -37,7 +37,7 @@
       md5sum: d41d8cd98f00b204e9800998ecf8427e
 
 - name: star align paired-end
-  command: nextflow run ./tests/software/star -entry test_star_alignment_paired_end -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/star/align -entry test_star_alignment_paired_end -c tests/config/nextflow.config
   tags:
     - star
     - star_align

tests/software/star/genomegenerate/test.yml

@@ -1,5 +1,5 @@
 - name: star genomegenerate
-  command: nextflow run ./tests/software/star -entry test_star_genomegenerate -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/star/genomegenerate -entry test_star_genomegenerate -c tests/config/nextflow.config
   tags:
     - star
     - star_genomegenerate

tests/software/ucsc/bedgraphtobigwig/test.yml

@@ -1,5 +1,5 @@
 - name: ucsc bedgraphtobigwig
-  command: nextflow run ./tests/software/ucsc/ -entry test_ucsc_bedgraphtobigwig -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/ucsc/bedgraphtobigwig -entry test_ucsc_bedgraphtobigwig -c tests/config/nextflow.config
   tags:
     - ucsc_bedgraphtobigwig
   files: