Snakefile

configfile: "config.yaml"
samplesfile = config["prefix"] + "/samples.tsv"
import pandas as pd

samples_df = pd.read_table(samplesfile).set_index("samples", drop=False)
sample_names = list(samples_df['samples'])



rule all:
  input:
    cx2_V_N=config['prefix']+"/cx_out/"+config["run_name"]+"/"+"normed_voted_cx_output.csv",
    dc2_V_N=config['prefix']+"/dc_out/"+config["run_name"]+"/"+"normed_voted_dc_output.csv",
    fc2_V_N=config['prefix']+"/fc_out/"+config["run_name"]+"/"+"normed_voted_fc_output.csv"



rule _r09_norm_circs:
  input:
    cx2_voted=config['prefix']+"/"+config["run_name"]+"ordered_circex_approved_by_all_three.csv",
    dc2_voted=config['prefix']+"/"+config["run_name"]+"ordered_dcc_approved_by_all_three.csv",
    fc2_voted=config['prefix']+"/"+config["run_name"]+"ordered_find_circ_approved_by_all_three.csv"
  params:
    norm_script=config['normalization_script'],
    reads_per_samplefile=config["prefix"]+"/reads_per_sample_"+config["run_name"]+".tsv"
  conda:
    "envs/parent_env.yaml"
  output:
    cx2_V_N=config['prefix']+"/cx_out/"+config["run_name"]+"/"+"normed_voted_cx_output.csv",
    dc2_V_N=config['prefix']+"/dc_out/"+config["run_name"]+"/"+"normed_voted_dc_output.csv",
    fc2_V_N=config['prefix']+"/fc_out/"+config["run_name"]+"/"+"normed_voted_fc_output.csv"
  shell:
    "Rscript {params.norm_script} {input.cx2_voted} {params.reads_per_samplefile} {output.cx2_V_N} && Rscript {params.norm_script} {input.fc2_voted} {params.reads_per_samplefile} {output.fc2_V_N} && Rscript {params.norm_script} {input.dc2_voted} {params.reads_per_samplefile} {output.dc2_V_N}"


# ad rule: vote and normalization
rule _r08_vote_circs:
  input:
    cx2_mat2=config['prefix']+"/cx_out/"+config["run_name"]+"/all_"+config["run_name"]+"_cx2.mat2",
    dc2_mat2=config['prefix']+"/dc_out/"+config["run_name"]+"/all_"+config["run_name"]+"_dcc2.mat2",
    fc2_mat2=config['prefix']+"/fc_out/"+config["run_name"]+"/all_"+config["run_name"]+"_fc2.mat2"
  params:
    r_script=config['voting_script'],
    dir_out=config['prefix'],
    run_name=config["run_name"],
  conda:
    "envs/parent_env.yaml"
  output:
    cx2_voted=config['prefix']+"/"+config["run_name"]+"ordered_circex_approved_by_all_three.csv",
    dc2_voted=config['prefix']+"/"+config["run_name"]+"ordered_dcc_approved_by_all_three.csv",
    fc2_voted=config['prefix']+"/"+config["run_name"]+"ordered_find_circ_approved_by_all_three.csv"
  shell:
    "cd {params.dir_out} && Rscript {params.r_script} {input.fc2_mat2} {input.cx2_mat2} {input.dc2_mat2} {params.run_name}"



rule _r07c_run_matrix2_cx:
  input:
    cx_hg38_mat1=config['prefix']+"/cx_out/"+config["run_name"]+"/all_"+config["run_name"]+"_cx2_tsvs.mat1"
  params:
    perl_script_mm2=config['mm2_script'],
    micrornas_file=config['micrornas_file'],
    coding_circnas_file=config['circbank_coding_file'],
    hallmarks_file=config['hallmarks_file'],
    ensembl_file=config['ensembl_file'],
    mapping_script=config['mapping_script']
  conda:
    "envs/parent_env.yaml"
  output:
    cx2_mat2=config['prefix']+"/cx_out/"+config["run_name"]+"/all_"+config["run_name"]+"_cx2.mat2"
  shell:
    "perl {params.perl_script_mm2} --i {input} --o {output} --m {params.micrornas_file} --c {params.coding_circnas_file} --h {params.hallmarks_file} --e {params.ensembl_file} --n {params.mapping_script} --e {params.ensembl_file} --excl_cb 1"



rule _r07b_run_matrix2_dc:
  input:
    dc_hg38_mat1=config['prefix']+"/dc_out/"+config["run_name"]+"/all_"+config["run_name"]+"_dcc2_tsvs.mat1"
  params:
    perl_script_mm2=config['mm2_script'],
    micrornas_file=config['micrornas_file'],
    coding_circnas_file=config['circbank_coding_file'],
    hallmarks_file=config['hallmarks_file'],
    ensembl_file=config['ensembl_file'],
    mapping_script=config['mapping_script']
  conda:
    "envs/parent_env.yaml"
  output:
    dc2_mat2=config['prefix']+"/dc_out/"+config["run_name"]+"/all_"+config["run_name"]+"_dcc2.mat2"
  shell:
    "perl {params.perl_script_mm2} --i {input} --o {output} --m {params.micrornas_file} --c {params.coding_circnas_file} --h {params.hallmarks_file} --e {params.ensembl_file} --n {params.mapping_script} --e {params.ensembl_file} --excl_cb 1"



rule _r07a_run_matrix2_fc:
  input:
    fc_hg38_mat1=config['prefix']+"/fc_out/"+config["run_name"]+"/all_"+config["run_name"]+"_fc2_tsvs.mat1"
  params:
    perl_script_mm2=config['mm2_script'],
    micrornas_file=config['micrornas_file'],
    coding_circnas_file=config['circbank_coding_file'],
    hallmarks_file=config['hallmarks_file'],
    ensembl_file=config['ensembl_file'],
    mapping_script=config['mapping_script']
  conda:
    "envs/parent_env.yaml"
  output:
    fc2_mat2=config['prefix']+"/fc_out/"+config["run_name"]+"/all_"+config["run_name"]+"_fc2.mat2"
  shell:
    "perl {params.perl_script_mm2} --i {input} --o {output} --m {params.micrornas_file} --c {params.coding_circnas_file} --h {params.hallmarks_file} --e {params.ensembl_file} --n {params.mapping_script} --e {params.ensembl_file} --excl_cb 1"


rule _r06c_run_matrixmaker_cx:
  input:
    all_cx_out_catted=config['prefix']+"/cx_out/"+config["run_name"]+"/all_"+config["run_name"]+"_cx2_tsvs.tx"
  params:
    perl_script_m1=config['mm1_script'],
    annotation_file_m1=config['mm1_refseq_file'],
    circs_bed_file=config['mm1_circ_bedfile']
  conda:
    "envs/parent_env.yaml"
  output:
    cx_hg38_mat1=config['prefix']+"/cx_out/"+config["run_name"]+"/all_"+config["run_name"]+"_cx2_tsvs.mat1"
  shell:
    "perl {params.perl_script_m1} --i {input} --o {output} --c {params.circs_bed_file} --g {params.annotation_file_m1}"



rule _r06b_run_matrixmaker_dc:
  input:
    all_dc_out_catted=config['prefix']+"/dc_out/"+config["run_name"]+"/all_"+config["run_name"]+"_dcc2_tsvs.tx"
  params:
    perl_script_m1=config['mm1_script'],
    annotation_file_m1=config['mm1_refseq_file'],
    circs_bed_file=config['mm1_circ_bedfile']
  conda:
    "envs/parent_env.yaml"
  output:
    dc_hg38_mat1=config['prefix']+"/dc_out/"+config["run_name"]+"/all_"+config["run_name"]+"_dcc2_tsvs.mat1"
  shell:
    "perl {params.perl_script_m1} --i {input} --o {output} --c {params.circs_bed_file} --g {params.annotation_file_m1}"




rule _r06a_run_matrixmaker_fc:
  input:
    all_fc2_out_catted=config['prefix']+"/fc_out/"+config["run_name"]+"/all_"+config["run_name"]+"_fc2_tsvs.tx"
  params:
    perl_script_m1=config['mm1_script'],
    annotation_file_m1=config['mm1_refseq_file'],
    circs_bed_file=config['mm1_circ_bedfile']
  conda:
    "envs/parent_env.yaml"
  output:
    fc_hg38_mat1=config['prefix']+"/fc_out/"+config["run_name"]+"/all_"+config["run_name"]+"_fc2_tsvs.mat1"
  shell:
    "perl {params.perl_script_m1} --i {input} --o {output} --c {params.circs_bed_file} --g {params.annotation_file_m1}"





rule _r05c_collect_tsvs_cx: # extend this rule to include outfiles from the last step respectively
  input:
    cx_outfiles=expand(config['prefix'] + "/cx_out/run_{name}" + "/processed_run_{name}.tsv",name=sample_names),
    reads_per_samplefile=config["prefix"]+"/reads_per_sample_"+config["run_name"]+".tsv" # to get the preparations to be executed
  params:
    run_name=config["run_name"]
  conda:
    "envs/parent_env.yaml"
  output:
    all_cx_out_catted=config['prefix']+"/cx_out/"+config["run_name"]+"/all_"+config["run_name"]+"_cx2_tsvs.tx"
  shell:
    "cat {input.cx_outfiles} >{output.all_cx_out_catted}"

rule _r05b_collect_tsvs_dc: # extend this rule to include outfiles from the last step respectively
  input:
    dc2_outfiles=expand(config['prefix'] + "/dc_out/run_{name}" + "/processed_run_{name}.tsv",name=sample_names),
    reads_per_samplefile=config["prefix"]+"/reads_per_sample_"+config["run_name"]+".tsv" # to get the preparations to be executed
  params:
    run_name=config["run_name"]
  conda:
    "envs/parent_env.yaml"
  output:
    all_dc_out_catted=config['prefix']+"/dc_out/"+config["run_name"]+"/all_"+config["run_name"]+"_dcc2_tsvs.tx"
  shell:
    "cat {input.dc2_outfiles} >{output.all_dc_out_catted}"

rule _r05a_collect_tsvs_fc: # extend this rule to include outfiles from the last step respectively
  input:
    fc2_outfiles=expand(config['prefix'] + "/fc_out/run_{name}" + "/processed_run_{name}.tsv",name=sample_names),
    reads_per_samplefile=config["prefix"]+"/reads_per_sample_"+config["run_name"]+".tsv" # to get the preparations to be executed
  params:
    run_name=config["run_name"]
  conda:
    "envs/parent_env.yaml"
  output:
    all_fc2_out_catted=config['prefix']+"/fc_out/"+config["run_name"]+"/all_"+config["run_name"]+"_fc2_tsvs.tx",

  shell:
    "cat {input.fc2_outfiles} >{output.all_fc2_out_catted}"


rule _r04_count_reads_fastqs:
  # make another new script
  input:
    infile=samplesfile,
    fastq_list_file=config["prefix"]+"/fastq_infiles_list.tx"
  params:
    dir_to_go=config["prefix"],
    run_name=config["run_name"],
    perl_script2=config["perl_script_dir"]+ "/fastq_list_to_reads_per_sample.pl",
    lane_1ident=config["lane_ident1"]
  conda:
    "envs/parent_env.yaml"
  output:
    reads_per_samplefile=config["prefix"]+"/reads_per_sample_"+config["run_name"]+".tsv"
  shell:
    "cd {params.dir_to_go} && perl {params.perl_script2} --l1 {params.lane_1ident} --i {input.fastq_list_file} >{output}"


# perl $perl_scripts_dir/fastq_list_to_infile_circs_ext.pl --i fastq_list_$proj_name.tx --g $proj_name --l1 $lane_diff --l2 $lane_to_id --m $paired_single_end_param >infile_$proj_name.tx
rule _r03_create_infile:
  input:
    fastq_list_file=config["prefix"]+"/fastq_infiles_list.tx"
  params:
    perl_script=config["perl_script_dir"]+ "/snake_infile_creator.pl",
    run_name=config["run_name"],
    lane_1ident=config["lane_ident1"],
    lane_2ident=config["lane_ident2"],
    dir_to_cd_to=config["prefix"]
  conda:
    "envs/parent_env.yaml"
  output:
    infile=config["prefix"] + "/samples.tsv" # workaround for now, delete the old infile before a new one get created
  shell:
    "rm -q {output} && cd {params.dir_to_cd_to} && perl {params.perl_script} --i {input} --l1 {params.lane_1ident} --l2 {params.lane_2ident} >{output}"

rule _r02_create_fastq_list:
  input:
    fc_2_chk_to_create=config["prefix"]+"/fc_out/"+config["run_name"]+"/chk.tx",
    cx_2_chk_to_create=config["prefix"]+"/cx_out/"+config["run_name"]+"/chk.tx",
    dc_2_chk_to_create=config["prefix"]+"/dc_out/"+config["run_name"]+"/chk.tx"
  params:
    dir_to_cd_to=config["prefix"]
  conda:
    "envs/parent_env.yaml"
  output:
    fastq_list_file=config["prefix"]+"/fastq_infiles_list.tx"
  shell:
    " cd {params.dir_to_cd_to} && ls -f1 *.fastq >{output}"


rule _r01_prepare_hg38_dirs:
  input:
    run_file="full_config_hg19.yaml"
  params:
    fc2_dir=config["prefix"]+"/fc_out/",
    dc2_dir=config["prefix"]+"/dc_out/",
    cx2_dir=config["prefix"]+"/cx_out/",
    fc_2_dir_to_create=config["prefix"]+"/fc_out/"+config["run_name"],
    cx_2_dir_to_create=config["prefix"]+"/cx_out/"+config["run_name"],
    dc_2_dir_to_create=config["prefix"]+"/dc_out/"+config["run_name"]
  conda:
    "envs/parent_env.yaml"
  output:
    # 3x chk.tx files, as before
    fc2_chk=config["prefix"]+"/fc_out/"+"chk.tx",
    dc2_chk=config["prefix"]+"/dc_out/"+"chk.tx",
    cx2_chk=config["prefix"]+"/cx_out/"+"chk.tx",
    fc_2_chk_to_create=config["prefix"]+"/fc_out/"+config["run_name"]+"/chk.tx",
    cx_2_chk_to_create=config["prefix"]+"/cx_out/"+config["run_name"]+"/chk.tx",
    dc_2_chk_to_create=config["prefix"]+"/dc_out/"+config["run_name"]+"/chk.tx"
  shell:
    "mkdir -p {params} && touch {output}"


include:"cx/Snakefile"
include:"dcc/Snakefile"
include:"f_c/Snakefile"