Нежелательная пустая строка в файле CSV

Вот как надежно (ваш существующий скрипт не будет работать для различных возможных входных значений) и обслуживаемо (если вы хотите добавить/удалить поля для печати или изменить их порядок, просто обновите первый split() аргумент) сделать то, что вы пытаетесь сделать, используя cat file вместо autorep -j $i -q, которого нет в моей системе:

$ cat tst.sh
#!/usr/bin/env bash

cat file |
awk '
    BEGIN {
        OFS = ","
        numTags = split("insert_job job_type box_name command machine owner date_conditions condition run_calendar exclude_calendar days_of_week run_window start_times start_mins resources profile term_run_time watch_file watch_interval",tags)
        for ( tagNr=1; tagNr<=numTags; tagNr++ ) {
            tag = tags[tagNr]
            printf "\"%s\"%s", tag, (tagNr<numTags ? OFS : ORS)
        }
    }

    !NF || /^/\*/ { next }
    { gsub(/^[[:space:]]+|[[:space:]]+$/,"") }

    match($0,/[[:space:]]job_type:/) {
        if ( jobNr++ ) {
            prt()
            delete tag2val
        }

        # save "insert_job" value
        tag = substr($1,1,length($1)-1)
        val = substr($0,length($1)+1,RSTART-(length($1)+2))
        gsub(/^[[:space:]]+|[[:space:]]+$/,"",val)
        tag2val[tag] = val

        # update $0 to start with "job_type" to look like all other input
        $0 = substr($0,RSTART+1)
    }

    {
        tag = val = $0
        sub(/:.*/,"",tag)
        sub(/[^:]+:[[:space:]]*/,"",val)
        tag2val[tag] = val
    }

    END { prt() }

    function prt(    tagNr,tag,val) {
        for ( tagNr=1; tagNr<=numTags; tagNr++ ) {
            tag = tags[tagNr]
            val = tag2val[tag]
            printf "\"%s\"%s", val, (tagNr<numTags ? OFS : ORS)
        }
    }
'

$ ./tst.sh
"insert_job","job_type","box_name","command","machine","owner","date_conditions","condition","run_calendar","exclude_calendar","days_of_week","run_window","start_times","start_mins","resources","profile","term_run_time","watch_file","watch_interval"
"Test_A","CMD","","sleep 3000","machine1","user1","0","","","","","","","","","","1","",""
"Test_B","CMD","","echo","machine2","user2","0","","","","","","","","","","","",""
"Test_c","CMD","","sleep 10","machine3","user3","0","","","","","","","","","","","",""
"Test_d","CMD","","ls","machine4","user4","0","","","","","","","","","","","",""

Вышеупомянутое является упрощенной версией моего ответа на ваш предыдущий вопрос, где я предоставил скрипт, который выводит CSV всех полей вместо приведенного выше, который выводит только определенный список полей.

Непонятно, почему у вас есть цикл, вызывающий autorep в вашем существующем скрипте, но если он вам по какой-то причине нужен, скорее всего, вы должны вызывать autorep в цикле и передавать вывод цикла в awk.

while IFS= read -r i; do
    autorep -j "$i" -q
done |
awk '...'

вместо вызова autorep и передачи его вывода в awk внутри цикла:

while IFS= read -r i; do
    autorep -j "$i" -q |
    awk '...'
done

Вышеприведенное было запущено на этой входной копии/вставленной из вашего вопроса:

$ cat file
/* ----------------- Test_A ----------------- */

insert_job: Test_A  job_type: CMD
command: sleep 3000
machine: machine1
owner: user1
permission:
date_conditions: 0
term_run_time: 1
alarm_if_fail: 1
alarm_if_terminated: 1


/* ----------------- Test_B ----------------- */

insert_job: Test_B    job_type: CMD
command: echo
machine: machine2
owner: user2
permission:
date_conditions: 0
description: "Test"
std_out_file: "/tmp/$AUTO_JOB_NAME.$AUTORUN.out"
std_err_file: "/tmp/$AUTO_JOB_NAME.$AUTORUN.err"
max_run_alarm: 1
alarm_if_fail: 0
alarm_if_terminated: 0
send_notification: 1



/* ----------------- Test_c ----------------- */

insert_job: Test_c   job_type: CMD
command: sleep 10
machine: machine3
owner: user3
permission:
date_conditions: 0
alarm_if_fail: 0
alarm_if_terminated: 0


/* ----------------- Test_d ----------------- */

insert_job: Test_d   job_type: CMD
command: ls
machine: machine4
owner: user4
permission:
date_conditions: 0
alarm_if_fail: 1
alarm_if_terminated: 1

Вот рубин для этого:

ruby -e '

scan1=/^/\*[ \ta-zA-Z_-]+\*/\R+([\s\S]*?)(?=(?:^/\*[ \t-]+)|\z)/
scan2=/([^ \t\n\r:]+): ([^ \t\n\r:]+)/

headers=  "insert_job   job_type    box_name    command machine owner   
        date_conditions condition   run_calendar    exclude_calendar    
        days_of_week    run_window  start_times start_mins  resources   
        profile term_run_time   watch_file  watch_interval".
        split.map{|e| "\"#{e}\""}

data=$<.read.
    scan(scan1).
    map{|block| block[0].scan(scan2)}

hsh=Hash.new {|h,k| h[k] = [""]*data.length}

data.each_with_index{|r,i|
    r.to_h.each{|k,v| hsh[k][i]=v}
}

puts headers.join(",")
hsh.values.transpose.
   each{|r| puts r.map{|e| e.match(/^".*"$/) ? e : "\"#{e}\""}.join(",")}

' file 

Отпечатки:

"insert_job","job_type","box_name","command","machine","owner","date_conditions","condition","run_calendar","exclude_calendar","days_of_week","run_window","start_times","start_mins","resources","profile","term_run_time","watch_file","watch_interval"
"Test_A","CMD","sleep","machine1","user1","0","1","1","1","","","","",""
"Test_B","CMD","echo","machine2","user2","0","","0","0","Test","/tmp/$AUTO_JOB_NAME.$AUTORUN.out","/tmp/$AUTO_JOB_NAME.$AUTORUN.err","1","1"
"Test_c","CMD","sleep","machine3","user3","0","","0","0","","","","",""
"Test_d","CMD","ls","machine4","user4","0","","1","1","","","","",""

И вот рубин, чтобы сделать второй:

ruby -e '
scan1=/(\S[\s\S]*?)(?=(?:^$)|\z)/
scan2=/(^[^:]+):[ \t]+(.*)/

data=$<.read.
    scan(scan1).
    map{|block| block[0].scan(scan2)}.
    map{|s| s.to_h}

hsh=Hash.new{|h,k| h[k] = [""]*data.length}
data.each_with_index{|h, i| h.each{|k,v| hsh[k][i]<<v}}

puts hsh.keys.map{|e| "\"#{e}\""}.join(",")
hsh.values.transpose.
    each{|r| puts r.map{|e| e.match(/^".*"$/) ? e : "\"#{e}\""}.join(",")}
' file 

Отпечатки:

"Machine Name","Type","Node Name","Agent Name","Operating System","Agent Release","Agent Build"
"machine1machine2","aa","machine1.testmachine2.test","AGENTAGENT","Windows Server 2012 Windows Server 2012 for amd64","12.012.0","6181, Service Pack 00, Maintenance Level 006181, Service Pack 00, Maintenance Level 00"
"machine1machine2","aa","machine1.testmachine2.test","AGENTAGENT","Windows Server 2012 Windows Server 2012 for amd64","12.012.0","6181, Service Pack 00, Maintenance Level 006181, Service Pack 00, Maintenance Level 00"