BAM trimming according to primers with ivar, new rule

resources/sars-cov-2/primers/nCoV-2019.primer.bed

@@ -0,0 +1,218 @@
+MN908947	30	54	nCoV-2019_1_LEFT	1	+
+MN908947	385	410	nCoV-2019_1_RIGHT	1	-
+MN908947	320	342	nCoV-2019_2_LEFT	2	+
+MN908947	704	726	nCoV-2019_2_RIGHT	2	-
+MN908947	642	664	nCoV-2019_3_LEFT	1	+
+MN908947	1004	1028	nCoV-2019_3_RIGHT	1	-
+MN908947	943	965	nCoV-2019_4_LEFT	2	+
+MN908947	1312	1337	nCoV-2019_4_RIGHT	2	-
+MN908947	1242	1264	nCoV-2019_5_LEFT	1	+
+MN908947	1623	1651	nCoV-2019_5_RIGHT	1	-
+MN908947	1573	1595	nCoV-2019_6_LEFT	2	+
+MN908947	1942	1964	nCoV-2019_6_RIGHT	2	-
+MN908947	1875	1897	nCoV-2019_7_LEFT	1	+
+MN908947	1868	1890	nCoV-2019_7_LEFT_alt0	1	+
+MN908947	2247	2269	nCoV-2019_7_RIGHT	1	-
+MN908947	2242	2264	nCoV-2019_7_RIGHT_alt5	1	-
+MN908947	2181	2205	nCoV-2019_8_LEFT	2	+
+MN908947	2568	2592	nCoV-2019_8_RIGHT	2	-
+MN908947	2505	2529	nCoV-2019_9_LEFT	1	+
+MN908947	2504	2528	nCoV-2019_9_LEFT_alt4	1	+
+MN908947	2882	2904	nCoV-2019_9_RIGHT	1	-
+MN908947	2880	2902	nCoV-2019_9_RIGHT_alt2	1	-
+MN908947	2826	2850	nCoV-2019_10_LEFT	2	+
+MN908947	3183	3210	nCoV-2019_10_RIGHT	2	-
+MN908947	3144	3166	nCoV-2019_11_LEFT	1	+
+MN908947	3507	3531	nCoV-2019_11_RIGHT	1	-
+MN908947	3460	3482	nCoV-2019_12_LEFT	2	+
+MN908947	3826	3853	nCoV-2019_12_RIGHT	2	-
+MN908947	3771	3795	nCoV-2019_13_LEFT	1	+
+MN908947	4142	4164	nCoV-2019_13_RIGHT	1	-
+MN908947	4054	4077	nCoV-2019_14_LEFT	2	+
+MN908947	4044	4068	nCoV-2019_14_LEFT_alt4	2	+
+MN908947	4428	4450	nCoV-2019_14_RIGHT	2	-
+MN908947	4402	4424	nCoV-2019_14_RIGHT_alt2	2	-
+MN908947	4294	4321	nCoV-2019_15_LEFT	1	+
+MN908947	4296	4322	nCoV-2019_15_LEFT_alt1	1	+
+MN908947	4674	4696	nCoV-2019_15_RIGHT	1	-
+MN908947	4666	4689	nCoV-2019_15_RIGHT_alt3	1	-
+MN908947	4636	4658	nCoV-2019_16_LEFT	2	+
+MN908947	4995	5017	nCoV-2019_16_RIGHT	2	-
+MN908947	4939	4966	nCoV-2019_17_LEFT	1	+
+MN908947	5296	5321	nCoV-2019_17_RIGHT	1	-
+MN908947	5230	5259	nCoV-2019_18_LEFT	2	+
+MN908947	5257	5287	nCoV-2019_18_LEFT_alt2	2	+
+MN908947	5620	5644	nCoV-2019_18_RIGHT	2	-
+MN908947	5620	5643	nCoV-2019_18_RIGHT_alt1	2	-
+MN908947	5563	5586	nCoV-2019_19_LEFT	1	+
+MN908947	5932	5957	nCoV-2019_19_RIGHT	1	-
+MN908947	5867	5894	nCoV-2019_20_LEFT	2	+
+MN908947	6247	6272	nCoV-2019_20_RIGHT	2	-
+MN908947	6167	6196	nCoV-2019_21_LEFT	1	+
+MN908947	6168	6197	nCoV-2019_21_LEFT_alt2	1	+
+MN908947	6528	6550	nCoV-2019_21_RIGHT	1	-
+MN908947	6526	6548	nCoV-2019_21_RIGHT_alt0	1	-
+MN908947	6466	6495	nCoV-2019_22_LEFT	2	+
+MN908947	6846	6873	nCoV-2019_22_RIGHT	2	-
+MN908947	6718	6745	nCoV-2019_23_LEFT	1	+
+MN908947	7092	7117	nCoV-2019_23_RIGHT	1	-
+MN908947	7035	7058	nCoV-2019_24_LEFT	2	+
+MN908947	7389	7415	nCoV-2019_24_RIGHT	2	-
+MN908947	7305	7332	nCoV-2019_25_LEFT	1	+
+MN908947	7671	7694	nCoV-2019_25_RIGHT	1	-
+MN908947	7626	7651	nCoV-2019_26_LEFT	2	+
+MN908947	7997	8019	nCoV-2019_26_RIGHT	2	-
+MN908947	7943	7968	nCoV-2019_27_LEFT	1	+
+MN908947	8319	8341	nCoV-2019_27_RIGHT	1	-
+MN908947	8249	8275	nCoV-2019_28_LEFT	2	+
+MN908947	8635	8661	nCoV-2019_28_RIGHT	2	-
+MN908947	8595	8619	nCoV-2019_29_LEFT	1	+
+MN908947	8954	8983	nCoV-2019_29_RIGHT	1	-
+MN908947	8888	8913	nCoV-2019_30_LEFT	2	+
+MN908947	9245	9271	nCoV-2019_30_RIGHT	2	-
+MN908947	9204	9226	nCoV-2019_31_LEFT	1	+
+MN908947	9557	9585	nCoV-2019_31_RIGHT	1	-
+MN908947	9477	9502	nCoV-2019_32_LEFT	2	+
+MN908947	9834	9858	nCoV-2019_32_RIGHT	2	-
+MN908947	9784	9806	nCoV-2019_33_LEFT	1	+
+MN908947	10146	10171	nCoV-2019_33_RIGHT	1	-
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+MN908947	10437	10459	nCoV-2019_34_RIGHT	2	-
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+MN908947	10737	10763	nCoV-2019_35_RIGHT	1	-
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+MN908947	11048	11074	nCoV-2019_36_RIGHT	2	-
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+MN908947	11927	11949	nCoV-2019_39_RIGHT	1	-
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+MN908947	13074	13096	nCoV-2019_43_RIGHT	1	-
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+MN908947	13007	13029	nCoV-2019_44_LEFT_alt3	2	+
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+MN908947	13363	13385	nCoV-2019_44_RIGHT_alt0	2	-
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+MN908947	13307	13336	nCoV-2019_45_LEFT_alt2	1	+
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+MN908947	13961	13984	nCoV-2019_46_RIGHT_alt2	2	-
+MN908947	13918	13946	nCoV-2019_47_LEFT	1	+
+MN908947	14271	14299	nCoV-2019_47_RIGHT	1	-
+MN908947	14207	14232	nCoV-2019_48_LEFT	2	+
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+MN908947	14545	14570	nCoV-2019_49_LEFT	1	+
+MN908947	14898	14926	nCoV-2019_49_RIGHT	1	-
+MN908947	14865	14895	nCoV-2019_50_LEFT	2	+
+MN908947	15224	15246	nCoV-2019_50_RIGHT	2	-
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+MN908947	15538	15560	nCoV-2019_51_RIGHT	1	-
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+MN908947	17065	17087	nCoV-2019_57_LEFT	1	+
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+MN908947	21357	21386	nCoV-2019_71_LEFT	1	+
+MN908947	21716	21743	nCoV-2019_71_RIGHT	1	-
+MN908947	21658	21682	nCoV-2019_72_LEFT	2	+
+MN908947	22013	22038	nCoV-2019_72_RIGHT	2	-
+MN908947	21961	21990	nCoV-2019_73_LEFT	1	+
+MN908947	22324	22346	nCoV-2019_73_RIGHT	1	-
+MN908947	22262	22290	nCoV-2019_74_LEFT	2	+
+MN908947	22626	22650	nCoV-2019_74_RIGHT	2	-
+MN908947	22516	22542	nCoV-2019_75_LEFT	1	+
+MN908947	22877	22903	nCoV-2019_75_RIGHT	1	-
+MN908947	22797	22819	nCoV-2019_76_LEFT	2	+
+MN908947	22798	22821	nCoV-2019_76_LEFT_alt3	2	+
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+MN908947	23189	23212	nCoV-2019_76_RIGHT_alt0	2	-
+MN908947	23122	23144	nCoV-2019_77_LEFT	1	+
+MN908947	23500	23522	nCoV-2019_77_RIGHT	1	-
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+MN908947	23789	23812	nCoV-2019_79_LEFT	1	+
+MN908947	24145	24169	nCoV-2019_79_RIGHT	1	-
+MN908947	24078	24100	nCoV-2019_80_LEFT	2	+
+MN908947	24443	24467	nCoV-2019_80_RIGHT	2	-
+MN908947	24391	24416	nCoV-2019_81_LEFT	1	+
+MN908947	24765	24789	nCoV-2019_81_RIGHT	1	-
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+MN908947	25969	25994	nCoV-2019_85_RIGHT	1	-
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+MN908947	27190	27215	nCoV-2019_89_RIGHT_alt4	1	-
+MN908947	27141	27164	nCoV-2019_90_LEFT	2	+
+MN908947	27511	27533	nCoV-2019_90_RIGHT	2	-
+MN908947	27446	27471	nCoV-2019_91_LEFT	1	+
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+MN908947	28394	28416	nCoV-2019_94_LEFT	2	+
+MN908947	28756	28779	nCoV-2019_94_RIGHT	2	-
+MN908947	28677	28699	nCoV-2019_95_LEFT	1	+
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+MN908947	28985	29007	nCoV-2019_96_LEFT	2	+
+MN908947	29356	29378	nCoV-2019_96_RIGHT	2	-
+MN908947	29288	29316	nCoV-2019_97_LEFT	1	+
+MN908947	29665	29693	nCoV-2019_97_RIGHT	1	-
+MN908947	29486	29510	nCoV-2019_98_LEFT	2	+
+MN908947	29836	29866	nCoV-2019_98_RIGHT	2	-

workflow/envs/ivar.yaml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - ivar=1.3.1

workflow/rules/trim_bam.smk

@@ -0,0 +1,40 @@
+import os
+
+__author__ = "Michal Okoniewski"
+__license__ = "Apache2.0"
+__maintainer__ = "Ivan Topolsky"
+__email__ = "v-pipe@bsse.ethz.ch"
+
+
+os.system(shellcommand)
+shellcommand="mkdir vtrim"
+
+# Assuming that getting the indexed BAMs from sam2bam in align.smk (ca l 427)
+
+
+rule ivar_trim:
+    input:
+        BAM="{file}.bam",
+        BAI="{file}.bam.bai",
+    output:
+        BAM="vtrim/{file}.bam",
+        BAI="vtrim/{file}.bam.bai"
+    params:
+        SAMTOOLS=config.applications["samtools"],
+        FUNCTIONS=functions,
+        BED_PRIMERS="resources/sars-cov-2/primers/nCoV-2019.primer.bed",
+    conda:
+       config.ivar["conda"],
+    threads: 1
+    shell:
+        """
+        echo "Trimming BAM with ivar"
+
+        ivar trim -e -i {input.BAM} -b {params.BED_PRIMERS} -p vtrim/unsorted_{wildcards.file}
+        {params.SAMTOOLS}  sort -o {output.BAM} -T out/{wildcards.file} {input.BAM}
+        {params.SAMTOOLS}  index {output.BAM}
+        rm vtrim/unsorted_{wildcards.file}.bam
+
+        """
+
+