Add extra test

Author: fgvieira

bio/mapdamage2/test/Snakefile

@@ -59,3 +59,33 @@ rule mapdamage2_rescale:
     threads: 1
     wrapper:
         "master/bio/mapdamage2"
+
+
+rule mapdamage2_all:
+    input:
+        bam="mapped/{sample}.bam",
+        ref="genome.fasta",
+    output:
+        GtoA3p="resultsall/{sample}.3pGtoA_freq.txt",
+        CtoT5p="resultsall/{sample}.5pCtoT_freq.txt",
+        dnacomp="resultsall/{sample}.dnacomp.txt",
+        lg_dist="resultsall/{sample}.lgdistribution.txt",
+        misinc="resultsall/{sample}.misincorporation.txt",
+        plot_misinc="resultsall/{sample}.Fragmisincorporation_plot.pdf",
+        plot_len="resultsall/{sample}.Length_plot.pdf",
+        stats_ref="results/all/{sample}.dnacomp_genome.csv",
+        stats_prob="results/all/{sample}.Stats_out_MCMC_correct_prob.csv",
+        stats_hist="results/all/{sample}.Stats_out_MCMC_hist.pdf",
+        stats_iter="results/all/{sample}.Stats_out_MCMC_iter.csv",
+        stats_summ="results/all/{sample}.Stats_out_MCMC_iter_summ_stat.csv",
+        stats_plot_pred="results/all/{sample}.Stats_out_MCMC_post_pred.pdf",
+        stats_plot_trace="results/all/{sample}.Stats_out_MCMC_trace.pdf",
+        bam="results/all/{sample}.bam",
+        log="results/all/{sample}.log",
+    params:
+        extra="--stats-only --burn 10 --iter 10",
+    log:
+        "logs/all/{sample}.log",
+    threads: 1
+    wrapper:
+        "master/bio/mapdamage2"

test_wrappers.py

@@ -134,7 +134,6 @@ def _run(wrapper, cmd, check_log=None, compare_results_with_expected=None):
     return _run
 
 
-
 def test_aria2c(run):
     run(
         "utils/aria2c",
@@ -1138,6 +1137,7 @@ def test_mapdamage2(run):
             "1",
             "--use-conda",
             "results/rescale/a.bam",
+            "results/all/a.bam",
         ],
     )
 
@@ -3301,11 +3301,25 @@ def test_fastq_screen(run):
     )
     run(
         "bio/fastq_screen",
-        ["snakemake", "--cores", "1", "qc/a.fastq_screen_conf.txt", "--use-conda", "-F"],
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "qc/a.fastq_screen_conf.txt",
+            "--use-conda",
+            "-F",
+        ],
     )
     run(
         "bio/fastq_screen",
-        ["snakemake", "--cores", "1", "qc/a.fastq_screen_nopng.txt", "--use-conda", "-F"],
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "qc/a.fastq_screen_nopng.txt",
+            "--use-conda",
+            "-F",
+        ],
     )
 
 
@@ -4333,6 +4347,7 @@ def test_samtools_fixmate(run):
         ["snakemake", "--cores", "1", "fixed/a.bam", "--use-conda", "-F"],
     )
 
+
 def test_pyfaidx(run):
     run(
         "bio/pyfaidx",
@@ -7060,6 +7075,7 @@ def test_mehari_annotate_seqvars(run):
         ],
     )
 
+
 def test_rasterio_clip_geotiff(run):
     run(
         "geo/rasterio/clip",
@@ -7071,7 +7087,6 @@ def test_rasterio_clip_geotiff(run):
             "-F",
             "results/montenegro.tiff",
             "results/switzerland.tiff",
-            "results/puerto_vallarta_small.tiff"
-        ]
-
+            "results/puerto_vallarta_small.tiff",
+        ],
     )