Add align after build_pop

cnvpipelines.py

@@ -705,13 +705,13 @@ class CnvPipeline:
                         raise FileExistsError(file + "already exists but is not a link")
                 os.symlink(file, final_link)
 
-            final_sample_file = os.path.join(self.wdir, "samples.list")
+            final_sample_file = os.path.join(self.wdir, "samples.yml")
             self.parse_align_sample_file(samples, final_sample_file)
 
             config = {
                 "wdir": self.wdir,
                 "reference": os.path.join(ref_dir, os.path.basename(reference)),
-                "sample_file": final_sample_file
+                "sample_file_align": final_sample_file
             }
 
             with open(self.config_file, "w") as config_file:
@@ -753,6 +753,17 @@ class CnvPipeline:
         if not os.path.exists(dest):
             os.symlink(source, dest)
 
+    @staticmethod
+    def _create_samples_fastq_simulaton(nb_inds, smple_file):
+        samples = {}
+        for i in range(1, nb_inds+1):
+            samples["indiv%d" % i] = {
+                "reads1": os.path.join("pop", "indiv%d_1.fq.gz" % i),
+                "reads2": os.path.join("pop", "indiv%d_2.fq.gz" % i)
+            }
+        with open(smple_file, "w") as samples_f:
+            yaml.dump(samples, samples_f, default_flow_style=False)
+
     def run_simulation(self, nb_inds, reference, nstretches, sv_list, coverage, force_polymorphism,
                        haploid, proba_del, proba_inv, read_len, insert_len_mean, insert_len_sd, min_deletions,
                        min_inversions, max_try, genotypes, force_wdir=False, **kwargs):
@@ -799,6 +810,10 @@ class CnvPipeline:
             ref_final = os.path.join(self.wdir, os.path.basename(reference))
             self._link(reference, ref_final)
 
+            # Create sample file for fastq files:
+            samples_file_fq = os.path.join(self.wdir, "samples.yml")
+            self._create_samples_fastq_simulaton(nb_inds, samples_file_fq)
+
             config = {
                 "wdir": self.wdir,
                 "nb_inds": nb_inds,
@@ -813,7 +828,8 @@ class CnvPipeline:
                 "insert_len_sd": insert_len_sd,
                 "min_deletions": min_deletions,
                 "min_inversions": min_inversions,
-                "max_try": max_try
+                "max_try": max_try,
+                "sample_file_align": samples_file_fq
             }
 
             nstretches_final = None

snakecnv/align.snk

@@ -13,7 +13,7 @@ from align_snakemake_utils import SnakemakeUtils
 
 
 # Get from config:
-samples = get_samples_align(config['sample_file'])
+samples = get_samples_align(config['sample_file_align'])
 reference = config['reference']
 wdir = config['wdir']
 
@@ -23,10 +23,10 @@ snakemake_utils = SnakemakeUtils(samples)
 
 include: "tools/threads.snk"
 
-localrules: all
+localrules: all_align
 
 
-rule all:
+rule all_align:
     input:
         expand("bams/{sample}.bam", sample=samples.keys()),
         expand("bams/{sample}.bam.bai", sample=samples.keys())

snakecnv/popsim.snk

@@ -54,7 +54,7 @@ def buildpop_inputs():
 def buildpop_outputs():
     outputs = []
     for n in range(1, NB_INDS+1):
-        outputs += [os.path.join("pop", "indiv%d_1.fq.gz" % n), os.path.join("pop", "indiv%d_2.fq.gz" % n)]
+        outputs += [os.path.abspath(os.path.join("pop", "indiv%d_1.fq.gz" % n)), os.path.abspath(os.path.join("pop", "indiv%d_2.fq.gz" % n))]
     return outputs
 
 bp_inputs, bp_params = buildpop_inputs()
@@ -62,12 +62,14 @@ bp_outputs = buildpop_outputs()
 
 
 include: "tools/threads.snk"
+include: "align.snk"
 
-localrules: all
+localrules: all_popsim
 
-rule all:
+rule all_popsim:
     input:
-        *bp_outputs
+        expand("bams/{sample}.bam", sample=["indiv%d" % i for i in range(1, NB_INDS+1)])
+        #*bp_outputs
 
 rule buildpop:
     input:
@@ -118,4 +120,4 @@ rule buildpop:
             command.append("-f")
         if params.haploid:
             command.append("-a")
-        shell(" ".join(command) + " 1> %s 2> %s" % (log.stdout, log.stderr))
\ No newline at end of file
+        shell(" ".join(command) + " 1> %s 2> %s" % (log.stdout, log.stderr))